Supported Applications
SAMtools
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Description
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
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Usage Notes
New samtools versions occasionally provide new features, remove older features or change options.
New versions of samtools are always made the default version in BioGrids/SBGrid.
For this reason, samtools versions should be explicitly set with a BioGrids/SBGrid version variable:
export SAMTOOLS=1.15
This ensures your workflows will continue to use the same version of samtools.
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Installation
Use the following command to install this title with the CLI client:$ biogrids-cli install samtools
Available operating systems: Linux 64, OS X INTEL -
Primary Citation*
H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000-Genome-Project-Data-Processing-Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16): 2078-2079.
P. Danecek, J. K. Bonfield, J. Liddle, J. Marshall, V. Ohan, M. O. Pollard, A. Whitwham, T. Keane, S. A. McCarthy, R. M. Davies, and H. Li. 2021. Twelve years of SAMtools and BCFtools. Gigascience. 10(2): giab008.
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*Full citation information available through
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Citation Note
Additional citation information can be found in the publication section of the SAMtools documentation page.
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Keywords
ChIP-Sequencing, DNA-Sequencing, High-throughput sequencing, RNA-Sequencing, WGS Analysis
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Default Versions
Linux 64:  1.17 (52.9 MB)
OS X INTEL:  1.17 (18.7 MB) -
Other Versions
Linux 64:
0.1.19 (2.7 MB) , 1.10 (10.4 MB) , 1.12 (1.0 GB) , 1.13 (450.5 MB) , 1.14 (675.1 MB) , 1.15 (283.6 MB) , 1.15.1 (103.8 MB) , 1.16 (52.7 MB) , 1.16.1 (52.7 MB) , 1.3 (3.6 MB) , 1.3.1 (3.6 MB) , 1.4.1 (12.5 MB) , 1.5 (19.1 MB) , 1.6 (81.9 MB) , 1.7 (16.4 MB) , 1.8 (6.5 MB) , 1.9 (6.9 MB) -
OS X INTEL:
0.1.19 (1.2 MB) , 1.10 (1.8 MB) , 1.12 (330.5 MB) , 1.13 (20.2 MB) , 1.14 (22.2 MB) , 1.15 (18.5 MB) , 1.15.1 (18.5 MB) , 1.16 (18.6 MB) , 1.16.1 (18.6 MB) , 1.3 (1.2 MB) , 1.3.1 (1.3 MB) , 1.4.1 (4.9 MB) , 1.5 (6.7 MB) , 1.6 (2.3 MB) , 1.7 (1.5 MB) , 1.8 (1.5 MB) , 1.9 (2.4 MB)
Developers
Bob Handshaker, Heng Li