Introduction

http://samtools.sourceforge.net/

http://sourceforge.net/projects/samtools/files/

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.

Usage

module load   bioinformatics/samtools/0.1.18

Installation

(SAMtools depends on the zlib library <http://www.zlib.net>. Version 1.2.3+ is
preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
file.)


module load library/zlib/1.2.5
mkdir /sw/samtools/0.1.18
cd /sw/samtools/0.1.18
make
make razip

Reference

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