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Google Keyword Rankings for : samtools software package
1
Samtools
http://www.htslib.org/
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/ ...
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http://www.htslib.org/
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/ ...
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2
Samtools - GitHub
https://github.com/samtools/samtools
(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.) Bug fixes: Fixed a ...
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https://github.com/samtools/samtools
(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.) Bug fixes: Fixed a ...
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3
SAMtools - Wikipedia
https://en.wikipedia.org/wiki/SAMtools
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence ... in August 2014 to split the SAMtools package into a stand-alone software ...
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https://en.wikipedia.org/wiki/SAMtools
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence ... in August 2014 to split the SAMtools package into a stand-alone software ...
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4
A Sample Software Installation – Samtools - FutureLearn
https://www.futurelearn.com/info/courses/linux-for-bioinformatics/0/steps/203633
Samtools is a suite of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary ...
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https://www.futurelearn.com/info/courses/linux-for-bioinformatics/0/steps/203633
Samtools is a suite of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary ...
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5
Sequence Alignment/Map format and SAMtools | Bioinformatics
https://academic.oup.com/bioinformatics/article/25/16/2078/204688
SAMtools is a library and software package for parsing and manipulating alignments in the SAM/BAM format. It is able to convert from other alignment formats, ...
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https://academic.oup.com/bioinformatics/article/25/16/2078/204688
SAMtools is a library and software package for parsing and manipulating alignments in the SAM/BAM format. It is able to convert from other alignment formats, ...
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6
SAMtools / BCFtools / HTSlib - Wellcome Sanger Institute
https://www.sanger.ac.uk/tool/samtools-bcftools-htslib/
SAMtools, BCFtools and HTSlib packages. HTSlib is a software library for manipulating various sequencing and variant file formats: SAM, BAM, CRAM, VCF, ...
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https://www.sanger.ac.uk/tool/samtools-bcftools-htslib/
SAMtools, BCFtools and HTSlib packages. HTSlib is a software library for manipulating various sequencing and variant file formats: SAM, BAM, CRAM, VCF, ...
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7
Installing SAMtools on Ubuntu - Bioinformatics Review
https://bioinformaticsreview.com/20210404/installing-samtools-on-ubuntu/
SAMtools is a software package for high-throughput sequencing data analysis [1]. It consists of three separate packages: SAMtools, BCFtools, ...
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https://bioinformaticsreview.com/20210404/installing-samtools-on-ubuntu/
SAMtools is a software package for high-throughput sequencing data analysis [1]. It consists of three separate packages: SAMtools, BCFtools, ...
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8
Samtools - encode
https://www.encodeproject.org/software/samtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools implements various utilities for post-processing alignments in ...
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https://www.encodeproject.org/software/samtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools implements various utilities for post-processing alignments in ...
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9
Bcftools by samtools
https://samtools.github.io/bcftools/
Bcftools. Manual page · Documentation · View the Project on GitHub samtools/bcftools · Download www.htslib.org. This is the official development repository ...
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https://samtools.github.io/bcftools/
Bcftools. Manual page · Documentation · View the Project on GitHub samtools/bcftools · Download www.htslib.org. This is the official development repository ...
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10
AUR (en) - samtools - Arch Linux
https://aur.archlinux.org/packages/samtools
I think that some warning in 3rd party software shouldn't prevent the package from installation. Regards. Rhinoceros commented on 2019-12-18 20:56 (UTC). Oops ...
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https://aur.archlinux.org/packages/samtools
I think that some warning in 3rd party software shouldn't prevent the package from installation. Regards. Rhinoceros commented on 2019-12-18 20:56 (UTC). Oops ...
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11
Install samtools on UNIX system - Easy Guides - Wiki - STHDA
http://www.sthda.com/english/wiki/install-samtools-on-unix-system
Samtools is a useful tool for manipulating and visualizing .bam files. ... Modify your .bashrc file so that when you type "samtools" it calls the program:.
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http://www.sthda.com/english/wiki/install-samtools-on-unix-system
Samtools is a useful tool for manipulating and visualizing .bam files. ... Modify your .bashrc file so that when you type "samtools" it calls the program:.
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12
Manipulating SAM/BAM alignment files - Homer
http://homer.ucsd.edu/homer/basicTutorial/samfiles.html
We will also discuss samtools, which is a free software package for ... BAM files are often the input files needed for many different analysis programs.
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http://homer.ucsd.edu/homer/basicTutorial/samfiles.html
We will also discuss samtools, which is a free software package for ... BAM files are often the input files needed for many different analysis programs.
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13
RRID:SCR_002105 - SciCrunch | Research Resource Resolver
https://scicrunch.org/resolver/SCR_002105
Description: Original SAMTOOLS package has been split into three separate ... data analysis software, software resource, data processing software, software ...
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https://scicrunch.org/resolver/SCR_002105
Description: Original SAMTOOLS package has been split into three separate ... data analysis software, software resource, data processing software, software ...
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14
Rsamtools - Bioconductor
https://bioconductor.org/packages/Rsamtools
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, ...
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https://bioconductor.org/packages/Rsamtools
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, ...
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15
Debian -- Details of package samtools in sid
https://packages.debian.org/sid/samtools
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM ...
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https://packages.debian.org/sid/samtools
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM ...
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16
samtools: SAM (Sequence/Alignment Mapping) Tools
https://hpcc.umd.edu/hpcc/help/software/samtools.html
Documentation for software package. ... SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, ...
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https://hpcc.umd.edu/hpcc/help/software/samtools.html
Documentation for software package. ... SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, ...
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17
SAMtools - bio.tools
https://bio.tools/samtools
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion ...
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https://bio.tools/samtools
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion ...
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18
Installation | Griffith Lab - Precision Medicine
https://pmbio.org/module-01-setup/0001/04/01/Software_Installation/
Install Samtools. Samtools is a software package based in C which provies utilities for manipulating alignment files (SAM/BAM/CRAM). It is open source, ...
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https://pmbio.org/module-01-setup/0001/04/01/Software_Installation/
Install Samtools. Samtools is a software package based in C which provies utilities for manipulating alignment files (SAM/BAM/CRAM). It is open source, ...
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19
SAMtools - Kennesaw State University HPC
https://hpcdocs.kennesaw.edu/modules/Software/SAMtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format ...
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https://hpcdocs.kennesaw.edu/modules/Software/SAMtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format ...
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20
How to Install SamTools, HTSLib, and BCFTools on Ubuntu ...
https://www.biostars.org/p/328831/
EDIT Wait, you're using apt-get to install prerequisites but not the actual software you need? Why is that? Pretty sure samtools is available on apt-get. ...
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https://www.biostars.org/p/328831/
EDIT Wait, you're using apt-get to install prerequisites but not the actual software you need? Why is that? Pretty sure samtools is available on apt-get. ...
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21
SAMtools - Sheffield HPC Documentation
https://docs.hpc.shef.ac.uk/en/latest/sharc/software/apps/SAMtools.html
simple enough to be easily generated by alignment programs or converted ... cp -r /usr/local/packages/apps/SAMtools/1.7/gcc-4.9.4/examples . cd examples ...
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https://docs.hpc.shef.ac.uk/en/latest/sharc/software/apps/SAMtools.html
simple enough to be easily generated by alignment programs or converted ... cp -r /usr/local/packages/apps/SAMtools/1.7/gcc-4.9.4/examples . cd examples ...
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22
Installing Samtools 1.3 With Code Examples
https://www.folkstalk.com/2022/09/installing-samtools-1-3-with-code-examples.html
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools.
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https://www.folkstalk.com/2022/09/installing-samtools-1-3-with-code-examples.html
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools.
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23
BAM parsing with samtools - by Aaron Quinlan - sandbox.bio
https://sandbox.bio/tutorials?id=samtools-intro
Our goal is to work through examples that demonstrate how to explore, process and manipulate SAM and BAM files with the samtools software package.
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https://sandbox.bio/tutorials?id=samtools-intro
Our goal is to work through examples that demonstrate how to explore, process and manipulate SAM and BAM files with the samtools software package.
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24
Samtools - Research Computing - Syracuse University
https://researchcomputing.syr.edu/samtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:.
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https://researchcomputing.syr.edu/samtools/
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:.
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25
Twelve years of SAMtools and BCFtools - PMC - NCBI
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931819/
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic ...
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931819/
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic ...
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26
Samtools 1.14 - CQLS Software Update List
https://software.cqls.oregonstate.edu/updates/samtools-1.14/
samtools. Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:.
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https://software.cqls.oregonstate.edu/updates/samtools-1.14/
samtools. Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:.
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27
SAMtools - SBGrid Consortium - Supported Software
https://sbgrid.org/software/titles/samtools
SAMtools · Description. (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for ...
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https://sbgrid.org/software/titles/samtools
SAMtools · Description. (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for ...
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28
Install Software from Source Code - UCSF Wynton HPC Cluster
https://wynton.ucsf.edu/hpc/howto/install-from-source.html
Lets use the HTSeq software samtools as a real-world example to ... 'cd' to the samtools-1.x directory containing the package's source and type the ...
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https://wynton.ucsf.edu/hpc/howto/install-from-source.html
Lets use the HTSeq software samtools as a real-world example to ... 'cd' to the samtools-1.x directory containing the package's source and type the ...
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29
Bioinformatics Tools | Install samtools by building from source
https://www.youtube.com/watch?v=ULQU8X3abxY
Bioinformatics Coach
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https://www.youtube.com/watch?v=ULQU8X3abxY
Bioinformatics Coach
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30
samtools - openSUSE Software
https://software.opensuse.org/package/samtools?locale=fa
Samtools implements various utilities for post-processing alignments in the SAM, BAM, ... There is no official package available for openSUSE Leap 15.4 ...
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https://software.opensuse.org/package/samtools?locale=fa
Samtools implements various utilities for post-processing alignments in the SAM, BAM, ... There is no official package available for openSUSE Leap 15.4 ...
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31
GigaDB Dataset - DOI 10.5524/100866 - GigaDB
http://www.gigadb.org/dataset/100866
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic ...
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http://www.gigadb.org/dataset/100866
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic ...
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32
swMATH - Samtools - Mathematical software
http://www.swmath.org/software/14583
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: ...
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http://www.swmath.org/software/14583
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: ...
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33
(How to) Install all software packages required to follow the ...
https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices
Software packages. BWA; SAMtools; Picard; Genome Analysis Toolkit (GATK); IGV; RStudio IDE and R libraries ggplot2 and gsalib.
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https://gatk.broadinstitute.org/hc/en-us/articles/360041320571--How-to-Install-all-software-packages-required-to-follow-the-GATK-Best-Practices
Software packages. BWA; SAMtools; Picard; Genome Analysis Toolkit (GATK); IGV; RStudio IDE and R libraries ggplot2 and gsalib.
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34
Use BWA, GATK, and SAMtools to perform gene sequencing
https://www.alibabacloud.com/help/en/e-hpc/latest/use-bwa-gatk-and-samtools-to-perform-high-performance-computing
Burrows-Wheeler Aligner (BWA) is a software package that maps low-divergent sequences against a large reference genome, such as the human genome ...
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https://www.alibabacloud.com/help/en/e-hpc/latest/use-bwa-gatk-and-samtools-to-perform-high-performance-computing
Burrows-Wheeler Aligner (BWA) is a software package that maps low-divergent sequences against a large reference genome, such as the human genome ...
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35
SAMtools - HPC User Wiki 2016 - Uni Oldenburg
https://wiki.hpcuser.uni-oldenburg.de/index.php?title=SAMtools
Samtools is a suite of programs for interacting with ... Samtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format ...
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https://wiki.hpcuser.uni-oldenburg.de/index.php?title=SAMtools
Samtools is a suite of programs for interacting with ... Samtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format ...
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36
samtools Tutorial - Quinlan Lab
http://quinlanlab.org/tutorials/samtools/samtools.html
... process and manipulate SAM and BAM files with the samtools software package. For future reference, use the samtools documentation.
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http://quinlanlab.org/tutorials/samtools/samtools.html
... process and manipulate SAM and BAM files with the samtools software package. For future reference, use the samtools documentation.
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37
Samtools - zbMATH Open
https://zbmath.org/software/14583
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/ ...
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https://zbmath.org/software/14583
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/ ...
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38
Play it again, SAMtools. Q&A with the SAMtools team on 12 ...
http://gigasciencejournal.com/blog/play-it-again-samtools/
The SAMtools suite of tools for manipulating sequencing data one of the most ... As recent signatories of the new Software Citation Guide ...
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http://gigasciencejournal.com/blog/play-it-again-samtools/
The SAMtools suite of tools for manipulating sequencing data one of the most ... As recent signatories of the new Software Citation Guide ...
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39
SAMtools - an overview | ScienceDirect Topics
https://www.sciencedirect.com/topics/medicine-and-dentistry/samtools
SAMtools program (http://samtools.sourceforge.net/) for manipulating BAM-formatted ... Toolkit package) and other software tools (Cornish and Guda, 2015).
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https://www.sciencedirect.com/topics/medicine-and-dentistry/samtools
SAMtools program (http://samtools.sourceforge.net/) for manipulating BAM-formatted ... Toolkit package) and other software tools (Cornish and Guda, 2015).
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40
Rsamtools - Bioconductor
http://bioconductor.riken.jp/packages/3.8/bioc/html/Rsamtools.html
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. Bioconductor version: 3.8. This package provides an interface to the 'samtools', ' ...
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http://bioconductor.riken.jp/packages/3.8/bioc/html/Rsamtools.html
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. Bioconductor version: 3.8. This package provides an interface to the 'samtools', ' ...
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41
The Sequence Alignment/Map format and SAMtools - Typeset.io
https://typeset.io/papers/the-sequence-alignment-map-format-and-samtools-4zxkoslnzd
SAMtools implements various utilities for post-processing alignments in the ... alignment can be achieved with the open source SAMtools software package.
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https://typeset.io/papers/the-sequence-alignment-map-format-and-samtools-4zxkoslnzd
SAMtools implements various utilities for post-processing alignments in the ... alignment can be achieved with the open source SAMtools software package.
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42
Documentation | Software | samtools - HPC@LSU
http://www.hpc.lsu.edu/docs/guides/software.php?software=samtools
About the Software. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating ...
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http://www.hpc.lsu.edu/docs/guides/software.php?software=samtools
About the Software. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating ...
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43
4.2.2.2. Installing samtools - Spider User Guide - Read the Docs
https://spiderdocs.readthedocs.io/en/latest/Pages/software/installing_samtools_on_project_space.html
Download the samtools packages in the Software space of the project: · Add the following line to export the following path in your $HOME/.bashrc: · Logout and ...
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https://spiderdocs.readthedocs.io/en/latest/Pages/software/installing_samtools_on_project_space.html
Download the samtools packages in the Software space of the project: · Add the following line to export the following path in your $HOME/.bashrc: · Logout and ...
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44
SAMtools - Veterans Affairs
https://www.oit.va.gov/Services/TRM/ToolPage.aspx?tid=15324
BAM files are typically compressed and more efficient for software to work ... Note: SAMtools is a suite that has two other components: BCFtools and HTSlib.
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https://www.oit.va.gov/Services/TRM/ToolPage.aspx?tid=15324
BAM files are typically compressed and more efficient for software to work ... Note: SAMtools is a suite that has two other components: BCFtools and HTSlib.
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45
SAMtools | Ohio Supercomputer Center
https://www.osc.edu/resources/available_software/software_list/samtools
SAMtools provide various utilities for manipulating alignments in the SAM format, ... Software. Fields of Science: Bioinformatics & Biology.
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https://www.osc.edu/resources/available_software/software_list/samtools
SAMtools provide various utilities for manipulating alignments in the SAM format, ... Software. Fields of Science: Bioinformatics & Biology.
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46
How to uninstall or remove samtools software package from ...
https://www.thelinuxfaq.com/ubuntu/ubuntu-17-04-zesty-zapus/samtools?type=uninstall
Uninstall samtools including dependent package. If you would like to remove samtools and it's dependent packages which are no longer needed from Ubuntu, $ sudo ...
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https://www.thelinuxfaq.com/ubuntu/ubuntu-17-04-zesty-zapus/samtools?type=uninstall
Uninstall samtools including dependent package. If you would like to remove samtools and it's dependent packages which are no longer needed from Ubuntu, $ sudo ...
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47
Software Asset Management (SAM) Tools Reviews and Ratings
https://www.gartner.com/reviews/market/software-asset-management-tools
The software asset management (SAM) tools are products that provide automation to support tasks required to produce and maintain compliance with independent ...
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https://www.gartner.com/reviews/market/software-asset-management-tools
The software asset management (SAM) tools are products that provide automation to support tasks required to produce and maintain compliance with independent ...
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48
SAMtools, BCFtools and HTSlib 1.2 | IZO-SGI Scientific ...
https://www.ehu.eus/sgi/scientific-software/samtools-bcftools-and-htslib-1-2
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools
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https://www.ehu.eus/sgi/scientific-software/samtools-bcftools-and-htslib-1-2
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools
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49
A Sample Software Installation - Samtools - StuDocu
https://www.studocu.com/en-gb/document/nottingham-trent-university/msc-bioinformatics/a-sample-software-installation-samtools-bioinformatics-for-biologists-wellcome-genome-campus-advanced-courses-and-scientific-conferences/22276540
Comments · Samtools is a suite of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM ...
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https://www.studocu.com/en-gb/document/nottingham-trent-university/msc-bioinformatics/a-sample-software-installation-samtools-bioinformatics-for-biologists-wellcome-genome-campus-advanced-courses-and-scientific-conferences/22276540
Comments · Samtools is a suite of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM ...
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50
samtoolsmpileup — Clara Parabricks v3.7 documentation
https://docs.nvidia.com/clara/parabricks/3.7.0/Documentation/ToolDocs/man_samtoolsmpileup.html
The command below is the samtools counterpart of the Parabricks command above. ... --version. View compatible software versions.
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https://docs.nvidia.com/clara/parabricks/3.7.0/Documentation/ToolDocs/man_samtoolsmpileup.html
The command below is the samtools counterpart of the Parabricks command above. ... --version. View compatible software versions.
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51
Bioconductor - Rsamtools - TU Dortmund
https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/html/Rsamtools.html
Binary alignment (BAM), variant call (BCF), or tabix file import ... This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see ...
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https://bioconductor.statistik.tu-dortmund.de/packages/2.12/bioc/html/Rsamtools.html
Binary alignment (BAM), variant call (BCF), or tabix file import ... This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see ...
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52
Bio-samtools 2: A package for analysis and visualization of ...
https://www.researchgate.net/publication/274261240_Bio-samtools_2_A_package_for_analysis_and_visualization_of_sequence_and_alignment_data_with_SAMtools_in_Ruby
PDF | bio-samtools is a Ruby language interface to SAMtools, ... 0.7.17 and then reformatted using the SAMtools software package v.
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https://www.researchgate.net/publication/274261240_Bio-samtools_2_A_package_for_analysis_and_visualization_of_sequence_and_alignment_data_with_SAMtools_in_Ruby
PDF | bio-samtools is a Ruby language interface to SAMtools, ... 0.7.17 and then reformatted using the SAMtools software package v.
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53
command_line_quiz2
http://binf.gmu.edu/swang36/NGS/command_line_quiz2.html
The resulting BAM file is included in the package 'gencommand_proj2_data.tar.gz'. Using SAMtools and BEDtools as well as other Unix commands ...
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http://binf.gmu.edu/swang36/NGS/command_line_quiz2.html
The resulting BAM file is included in the package 'gencommand_proj2_data.tar.gz'. Using SAMtools and BEDtools as well as other Unix commands ...
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54
Harwood Lab - Xpression - University of Washington
https://depts.washington.edu/cshlab/xpression/html/install.shtml
samtools 0.1.10+. Python packages: pysam 0.3+; Biopython 1.51+. GUI software: Java Runtime Environment (JRE) 1.5+. Install from ...
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https://depts.washington.edu/cshlab/xpression/html/install.shtml
samtools 0.1.10+. Python packages: pysam 0.3+; Biopython 1.51+. GUI software: Java Runtime Environment (JRE) 1.5+. Install from ...
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55
SAMtools | PSC
https://www.psc.edu/resources/software/samtools/
SAMTools. SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments ...
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https://www.psc.edu/resources/software/samtools/
SAMTools. SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments ...
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56
Run natively - PEPATAC
http://pepatac.databio.org/en/latest/detailed-install/
This guide walks you through the nitty-gritty of how to install each prerequisite package. 1. Install required software. Python packages. The pipeline uses ...
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http://pepatac.databio.org/en/latest/detailed-install/
This guide walks you through the nitty-gritty of how to install each prerequisite package. 1. Install required software. Python packages. The pipeline uses ...
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57
Preseq | The Smith Lab
http://smithlabresearch.org/software/preseq/
The preseq package is aimed at predicting and estimating the complexity of a genomic ... This functionality, which is called gc_extrap in the software, ...
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http://smithlabresearch.org/software/preseq/
The preseq package is aimed at predicting and estimating the complexity of a genomic ... This functionality, which is called gc_extrap in the software, ...
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58
Rsamtools - Bioconductor
https://ftp.gwdg.de/pub/misc/bioconductor/packages/2.9/bioc/html/Rsamtools.html
Binary alignment (BAM), variant call (BCF), or tabix file import ... This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see ...
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https://ftp.gwdg.de/pub/misc/bioconductor/packages/2.9/bioc/html/Rsamtools.html
Binary alignment (BAM), variant call (BCF), or tabix file import ... This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see ...
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59
Parsing and analyzing BAM files - Renesh Bedre
https://www.reneshbedre.com/blog/handle-analyze-bam-files.html
SAMtools, a software package, allows parsing and analyzing the SAM/BAM files. Here, I am using SAMtools v1.15.
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https://www.reneshbedre.com/blog/handle-analyze-bam-files.html
SAMtools, a software package, allows parsing and analyzing the SAM/BAM files. Here, I am using SAMtools v1.15.
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60
Running SAMtools Commands - HCC-DOCS
https://hcc.unl.edu/docs/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands/
[sam|bam] file is the converted file into SAM or BAM format respectively. Running samtools view on Crane with 8 CPUs , input file input_alignments.sam with ...
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https://hcc.unl.edu/docs/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands/
[sam|bam] file is the converted file into SAM or BAM format respectively. Running samtools view on Crane with 8 CPUs , input file input_alignments.sam with ...
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61
xsamtools - PyPI
https://pypi.org/project/xsamtools/
xsamtools makes the samtools tooling from htslib and bcftools available through pypi packaging. These tools have been lightly modified to allow merges on ...
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https://pypi.org/project/xsamtools/
xsamtools makes the samtools tooling from htslib and bcftools available through pypi packaging. These tools have been lightly modified to allow merges on ...
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62
Variant Calling with SAMtools | DNA Sequencing Software
http://www.genecodes.com/variant-calling-with-samtools
› variant-calling-with-samto...
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http://www.genecodes.com/variant-calling-with-samtools
› variant-calling-with-samto...
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63
[2012.10295] Twelve years of SAMtools and BCFtools - arXiv
https://arxiv.org/abs/2012.10295
The SAMtools and BCFtools packages represent a unique collection of ... in numerous other software projects and countless genomic pipelines.
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https://arxiv.org/abs/2012.10295
The SAMtools and BCFtools packages represent a unique collection of ... in numerous other software projects and countless genomic pipelines.
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64
Install samtools github - shoppingday.shop
https://jdwj.shoppingday.shop/vxu.html
Install Samtools. Samtools is a software package based in C which provies utilities for manipulating alignment files (SAM/BAM/CRAM). It is open source, ...
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https://jdwj.shoppingday.shop/vxu.html
Install Samtools. Samtools is a software package based in C which provies utilities for manipulating alignment files (SAM/BAM/CRAM). It is open source, ...
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65
The Sequence Alignment/ Map Format and SAMtools
https://pdfs.semanticscholar.org/3e53/2ce53a69ee883470f4ae232afad70a1b65c8.pdf
In this article, we present an overview of the SAM format and briefly introduce the companion SAMtools software package. A detailed format specification and the ...
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https://pdfs.semanticscholar.org/3e53/2ce53a69ee883470f4ae232afad70a1b65c8.pdf
In this article, we present an overview of the SAM format and briefly introduce the companion SAMtools software package. A detailed format specification and the ...
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66
TopHat - CCB at JHU - Johns Hopkins University
https://ccb.jhu.edu/software/tophat/
removed SAMtools as an external dependency in order to avoid ... and its code library (an older, stable SAMtools version is now packaged with TopHat) ...
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https://ccb.jhu.edu/software/tophat/
removed SAMtools as an external dependency in order to avoid ... and its code library (an older, stable SAMtools version is now packaged with TopHat) ...
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67
List of Bioinformatics Software Tools for Next Generation ... - BOL
https://bioinformaticsonline.com/pages/revision/2414
Samtools BAQ), the likelihoods combine with individual-based prior ... Description: software package, SNV calling from normal-tumor pair and ...
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https://bioinformaticsonline.com/pages/revision/2414
Samtools BAQ), the likelihoods combine with individual-based prior ... Description: software package, SNV calling from normal-tumor pair and ...
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68
Algorithm User Guide for RVD
https://dna-discovery.stanford.edu/publicmaterial/software/rvd/AlgorithmUserGuide.pdf
The RVD program takes BAM files of deep sequencing reads in as input. ... If you do not have samtools 0.1.18, download and install the program package:.
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https://dna-discovery.stanford.edu/publicmaterial/software/rvd/AlgorithmUserGuide.pdf
The RVD program takes BAM files of deep sequencing reads in as input. ... If you do not have samtools 0.1.18, download and install the program package:.
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69
Software supported by NCGAS - IU KB
https://kb.iu.edu/d/bdko
› bdko
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https://kb.iu.edu/d/bdko
› bdko
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70
Twelve years of SAMtools and BCFtools - University of Glasgow
https://eprints.gla.ac.uk/254020/1/254020.pdf
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and ...
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https://eprints.gla.ac.uk/254020/1/254020.pdf
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and ...
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71
SAMTOOLS - Bioinformatics Team (BioITeam) at the ...
https://wikis.utexas.edu/display/bioiteam/SAMTOOLS
1. samtools idxstats : This tool will provide statistics about how many reads have aligned to each sequence/chromosome in the reference genome.
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https://wikis.utexas.edu/display/bioiteam/SAMTOOLS
1. samtools idxstats : This tool will provide statistics about how many reads have aligned to each sequence/chromosome in the reference genome.
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72
Documentation | Software | samtools - LONI HPC
http://hpc.loni.org/docs/guides/software.php?software=samtools&machine=qb3
About the Software. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, ...
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http://hpc.loni.org/docs/guides/software.php?software=samtools&machine=qb3
About the Software. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, ...
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73
howto Install all software packages required to follow the ...
https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/tutorials/2899-howto-install-all-software-packages-required-to-follow-the-gatk-best-practices
Software packages. BWA; SAMtools; Picard; Genome Analysis Toolkit (GATK); IGV; RStudio IDE and R libraries ggplot2 and gsalib. Note that the version numbers ...
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https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/tutorials/2899-howto-install-all-software-packages-required-to-follow-the-gatk-best-practices
Software packages. BWA; SAMtools; Picard; Genome Analysis Toolkit (GATK); IGV; RStudio IDE and R libraries ggplot2 and gsalib. Note that the version numbers ...
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74
samtools/1.9 — Research Computing Center Manual
https://rcc.uchicago.edu/docs/software/modules/samtools/midway2/1.9.html
Full list of software modules available on Midway. Software Modules Tutorial: A tutorial on Midway modules and how to use them.
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https://rcc.uchicago.edu/docs/software/modules/samtools/midway2/1.9.html
Full list of software modules available on Midway. Software Modules Tutorial: A tutorial on Midway modules and how to use them.
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75
Whole genome sequence analysis for novices
http://wbg.wormbook.org/2012/06/25/whole-genome-sequence-analysis-for-novices/
Variant identification: The SAMtools software package was used to identify variants and call genotypes based on SAM alignment files ...
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http://wbg.wormbook.org/2012/06/25/whole-genome-sequence-analysis-for-novices/
Variant identification: The SAMtools software package was used to identify variants and call genotypes based on SAM alignment files ...
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76
Performance Analysis and Optimization of SAMtools Sorting
https://link.springer.com/chapter/10.1007/978-3-319-58943-5_33
SAMtools is a suite of tools that is widely-used in genomics workflows for post-processing sequence alignment data from large ...
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https://link.springer.com/chapter/10.1007/978-3-319-58943-5_33
SAMtools is a suite of tools that is widely-used in genomics workflows for post-processing sequence alignment data from large ...
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77
SAMtools - Wikiwand
https://www.wikiwand.com/en/SAMtools
SAMtools makes it possible to work directly with a compressed BAM file ... to split the SAMtools package into a stand-alone software library ...
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https://www.wikiwand.com/en/SAMtools
SAMtools makes it possible to work directly with a compressed BAM file ... to split the SAMtools package into a stand-alone software library ...
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78
Ruby bindings for SAMtools, a library for accessing BAM files ...
https://d-nb.info/1235753808/34
Background: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, ...
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https://d-nb.info/1235753808/34
Background: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, ...
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79
Week 6: Mapping with Bowtie2 - Protocols.io
https://www.protocols.io/view/week-6-mapping-with-bowtie2-g5zby76
samtools view is one program within the whole samtools package. The flag “-bS” is not BS. It means convert a bam file to a sam file. (Bioinformatics ...
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https://www.protocols.io/view/week-6-mapping-with-bowtie2-g5zby76
samtools view is one program within the whole samtools package. The flag “-bS” is not BS. It means convert a bam file to a sam file. (Bioinformatics ...
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80
Variant Calling Workflow - Data Carpentry
https://datacarpentry.org/wrangling-genomics/04-variant_calling/index.html
We will convert the SAM file to BAM format using the samtools program with the ... instructions for more information on installing these software packages.
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https://datacarpentry.org/wrangling-genomics/04-variant_calling/index.html
We will convert the SAM file to BAM format using the samtools program with the ... instructions for more information on installing these software packages.
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81
Twelve years of SAMtools and BCFtools | Papers With Code
https://paperswithcode.com/paper/twelve-years-of-samtools-and-bcftools
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and ...
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https://paperswithcode.com/paper/twelve-years-of-samtools-and-bcftools
The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and ...
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82
Galaxy |
https://toolshed.g2.bx.psu.edu/repository/view_repository?changeset_revision=7254ece0c0ff&id=6ae6c168e90c9466
Internally this tool uses the command-line samtools suite. ... person obtaining a copy of this software and associated documentation files (the "Software"), ...
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https://toolshed.g2.bx.psu.edu/repository/view_repository?changeset_revision=7254ece0c0ff&id=6ae6c168e90c9466
Internally this tool uses the command-line samtools suite. ... person obtaining a copy of this software and associated documentation files (the "Software"), ...
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83
Samtools - Linux Mint - Community
https://community.linuxmint.com/software/view/samtools
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM ...
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https://community.linuxmint.com/software/view/samtools
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM ...
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84
pegi3s/samtools_bcftools - Docker Image
https://hub.docker.com/r/pegi3s/samtools_bcftools/
(Please note that the original software licenses still apply). This image facilitates the usage of SAMtools-BCFtools, a suite of programs for interacting with ...
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https://hub.docker.com/r/pegi3s/samtools_bcftools/
(Please note that the original software licenses still apply). This image facilitates the usage of SAMtools-BCFtools, a suite of programs for interacting with ...
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85
cannot configure or make install samtools 0.1.19 - Ask Ubuntu
https://askubuntu.com/questions/1095711/cannot-configure-or-make-install-samtools-0-1-19
It is packaged in all currently supported versions in universe pocket. ... samtools Program: samtools (Tools for alignments in the SAM ...
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https://askubuntu.com/questions/1095711/cannot-configure-or-make-install-samtools-0-1-19
It is packaged in all currently supported versions in universe pocket. ... samtools Program: samtools (Tools for alignments in the SAM ...
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86
samtools - Bioinformatic tools - Truwl
https://truwl.com/tools/library/samtools/1.x
A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.
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https://truwl.com/tools/library/samtools/1.x
A software package with various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.
→ Check Latest Keyword Rankings ←
87
Samtools guide: learning how to filter and manipulate with ...
https://medium.com/@shilparaopradeep/samtools-guide-learning-how-to-filter-and-manipulate-with-sam-bam-files-2c28b25d29e8
Samtools is a set of utilities that manipulate alignments in the BAM format. ... how to manipulate with BAM files with samtools — an excellent suite of ...
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https://medium.com/@shilparaopradeep/samtools-guide-learning-how-to-filter-and-manipulate-with-sam-bam-files-2c28b25d29e8
Samtools is a set of utilities that manipulate alignments in the BAM format. ... how to manipulate with BAM files with samtools — an excellent suite of ...
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88
Tool Installation | Griffith Lab - RNA-seq
https://rnabio.org/module-00-setup/0000/10/01/Installation/
samtools bam-readcount Installation type: build C++ binary from source code ... a python package that can be installed using the linux package manager apt.
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https://rnabio.org/module-00-setup/0000/10/01/Installation/
samtools bam-readcount Installation type: build C++ binary from source code ... a python package that can be installed using the linux package manager apt.
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89
bam.read in mskilab/skidb: Collection of R functions ... - Rdrr.io
https://rdrr.io/github/mskilab/skidb/man/bam.read.html
... to csv via samtools call (instead of Rsamtools like read.bam) ... file dumps of common databases and external software used by @mskilab.
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https://rdrr.io/github/mskilab/skidb/man/bam.read.html
... to csv via samtools call (instead of Rsamtools like read.bam) ... file dumps of common databases and external software used by @mskilab.
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90
How to install samtools on Ubuntu
https://howtoinstall.co/en/samtools
Installing samtools package on Ubuntu is as easy as running the following command ... Advanced Package Tool, or APT, is a free software user interface that ...
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https://howtoinstall.co/en/samtools
Installing samtools package on Ubuntu is as easy as running the following command ... Advanced Package Tool, or APT, is a free software user interface that ...
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91
Picard Tools | The Minnesota Supercomputing Institute
https://www.msi.umn.edu/sw/picard-tools
The SAMtools software package provides similar functionality. ... The Picard command-line tools are packaged as executable jar files.
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https://www.msi.umn.edu/sw/picard-tools
The SAMtools software package provides similar functionality. ... The Picard command-line tools are packaged as executable jar files.
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92
Alignment of NGS reads, samtools and visualization
http://wikis.babelomics.org/gda16/lib/exe/fetch.php/hands-on.gda2016.pdf
Alignment of NGS reads, samtools and visualization. Hands-on. Software used in this practical. ○ BWA MEM : Burrows-Wheeler Aligner. A software package for ...
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http://wikis.babelomics.org/gda16/lib/exe/fetch.php/hands-on.gda2016.pdf
Alignment of NGS reads, samtools and visualization. Hands-on. Software used in this practical. ○ BWA MEM : Burrows-Wheeler Aligner. A software package for ...
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93
client_CLI_usage
https://biogrids.org/wiki/client_CLI_usage
The BioGrids software installation client is a command line-based installer for ... biogrids info samtools Package: SAMtools Name slug: samtools Available ...
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https://biogrids.org/wiki/client_CLI_usage
The BioGrids software installation client is a command line-based installer for ... biogrids info samtools Package: SAMtools Name slug: samtools Available ...
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94
Samtools Introduction Version 0.1.19 General Tips
https://stab.st-andrews.ac.uk/wiki/index.php?title=Samtools&action=pdfbook&format=single
This is due to the fact that samtools is a suite of tools for handling ... as this is samtools' software brief, to be able to thandle the file format.
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https://stab.st-andrews.ac.uk/wiki/index.php?title=Samtools&action=pdfbook&format=single
This is due to the fact that samtools is a suite of tools for handling ... as this is samtools' software brief, to be able to thandle the file format.
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