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Diffstat (limited to 'academic/samtools/README')
| -rw-r--r-- | academic/samtools/README | 29 |
1 files changed, 9 insertions, 20 deletions
diff --git a/academic/samtools/README b/academic/samtools/README index 0203586f94..ea600cbe26 100644 --- a/academic/samtools/README +++ b/academic/samtools/README @@ -1,22 +1,11 @@ -SAM (Sequence Alignment/Map) format is a generic format for storing -large nucleotide sequence alignments. SAM aims to be a format that: +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 -- 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. +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. -SAM Tools provide various utilities for manipulating alignments in the -SAM format, including sorting, merging, indexing and generating -alignments in a per-position format. - -Publication: -Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., -Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data -Processing Subgroup (2009) The Sequence alignment/map (SAM) format and -SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] +Note that the sam.h of htslib differs from sam.h coming with samtools. |