SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that- Is flexible enough to store all the alignment information generated by various alignment programs;- Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;- Is compact in file size;- Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;- Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Version: 1.3.1(Marconi)1.13(G100)

Availability: GALILEO100, MARCONI

Target: all

Official web site:

Related Commands:

module load profile/bioinf
module load autoload samtools

Help and Documentation:

How to use: