academic/samtools-legacy: Added (Sequence Alignment/Map Tools).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 28 insertions, 0 deletions

diff --git a/academic/samtools-legacy/README b/academic/samtools-legacy/README
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+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.
+
+NOTE!
+This is an older version of the program, kept here for compatibility
+with Ugene. You can safely install it along the new one. When you start
+Ugene, go to Settings > Preferences > External Tools and manually select
+the legacy binaries in /usr/bin/
+
+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]