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SAM (Sequence Alignment/Map) format is a generic format for storing large
nucleotide sequence alignments. The original samtools package has been split
into three separate but tightly coordinated projects: htslib (C library for
handling high-throughput sequencing data), samtools (for handling SAM, BAM,
CRAM), and bcftools (for handling VCF and BCF).
Samtools is now distributed as an individual package. Installation is set up
so that the code uses an external HTSlib (also at SBo). Although deprecated
upstream, in the case that people need parts of samtools-legacy (e.g header
files or libbam) these can be installed from this package by modifying the
samtools.Slackbuild. Note that the sam.h of htslib differs from sam.h coming
with samtools.
Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed
in a single samtools-0.1.x package. This old version remains available from
SBo as samtools-legacy.
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