aboutsummaryrefslogtreecommitdiff
path: root/academic/samtools/README
diff options
context:
space:
mode:
authorPetar Petrov <petar.petrov@student.oulu.fi>2013-12-14 08:02:52 +0700
committerErik Hanson <erik@slackbuilds.org>2013-12-14 10:53:05 -0600
commit00017f6260e9e0d2951eac42aeea9d8fbb9f1034 (patch)
treeed8db6c055c2fc57e4f322ececdf77392e77c6d3 /academic/samtools/README
parent723d17ef4fdabd19a8004eb40ec1864d78082c8c (diff)
academic/samtools: Added (Sequence Alignment/Map Tools).
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/samtools/README')
-rw-r--r--academic/samtools/README22
1 files changed, 22 insertions, 0 deletions
diff --git a/academic/samtools/README b/academic/samtools/README
new file mode 100644
index 000000000000..0203586f9426
--- /dev/null
+++ b/academic/samtools/README
@@ -0,0 +1,22 @@
+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.
+
+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]