SAMtools

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Description

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. 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.

Availability

Verze 0.1.18, 0.1.19, 1.2, 1.3, 1.3.1 and 1.4. Available modules:

samtools-0.1.18
samtools-0.1.18alt
samtools-0.1.19
samtools-0.1.19fPIC
samtools-1.2
samtools-1.3
samtools-1.3.1
samtools-1.4

Use

module add samtools-1.3.1
samtools

for more details see Documentation. Module samtools-0.1.18alt is compiled with -fPIC.

Documentation

http://www.htslib.org/doc/#manual-pages

Licence

The MIT/Expat License

Program manager

meta@cesnet.cz

Homepage

http://samtools.sourceforge.net/
http://www.htslib.org/