Samtools provides utilities for manipulating alignments in the Sequence Alignment/Map (SAM) format, including sorting, merging, indexing and generating alignments in a per-position format.It also includes an aligment viewer.

The SAM format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible, compact and efficient. Alignments from the 1000 Genomes Project are released in SAM format.

The samtools package is prepared by Debian-med and can be installed on Bio-Linux by typing:

There are numerous scripts and programs that come in the samtools package. You can find out more by referring to the man page: after installing samtools, type: man samtools or by referring to the remote documentation.

Other tools available on Bio-Linux for handling data from new sequencing technologies are described in the bioinformatics documentation on the NEBC website.