Join us

Supported Applications

SAMtools

  • 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.

  • 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.

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install samtools Copy to clipboard 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.


    • *Full citation information available through

  • Citation Note

    Additional citation information can be found in the publication section of the SAMtools documentation page.

  • Keywords

    ChIP-Sequencing, DNA-Sequencing, High-throughput sequencing, RNA-Sequencing, WGS Analysis

  • 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

Scroll