The Sequence Alignment/Map format and SAMtools.

by: Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup

Bioinformatics (Oxford, England), Vol. 25, No. 16. (15 August 2009), pp. 2078-2079.

Abstract

SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.

View the full article here:

DOI, HighWire, HighWire (PDF), HighWire, Pubmed, Hubmed

This article has been bookmarked 32 times, initially on 2009-06-09.

2009-12-14	User MarkFiers
	no-tag
2009-12-07	User darian
	next-generation-sequencing, applications, alignment-based
2009-11-17	User cthachuk
	tool, software, ngs, file-format
2009-11-16	User hzoltan
	no-tag
2009-11-02	User seb1
	viewer, short-read
	User heliopais
	read-mapping, high-throughput-sequencing
2009-10-12	User urgi
	short-reads, format, algorithm
2009-09-28	User idonaldson
	tool, ngs
2009-08-21	User GustavoLacerda
	ngs
2009-08-19	User stubrown
	software, nextgen, keypaper
2009-08-17	User cassj
	sequencing, samtools, sam, ngs, nextgen, format, bam
	User kshameer
	standard, next-generation-sequencing, alignment
2009-08-15	User ciax
	sequencealignment
2009-08-10	Group BergmanLab
	add, alignment, hts
	User polivares
	alignment, hts
2009-08-08	User carlosjavierna
	sequences
2009-08-07	User jandot
	alignment, samtools
2009-08-04	User katholt
	no-tag
2009-07-26	User jmcq
	no-tag
	User guhjy
	alignment, software, seq
2009-07-12	User orzenil
	ngs, short_reads
2009-07-02	User jasontsai
	ngs, short-read-mapping
2009-06-30	User operon
	assembly, bioinformatics, genomics, method, software
2009-06-17	User farhat
	no-tag
2009-06-15	Group Journal picks
	nextgenerationsequencing
	User AlexBateman
	nextgenerationsequencing
2009-06-12	User chrisamiller
	alignment, genomic, mapping, sequence, snp, utility
2009-06-10	User nuin
	alignment, sequence
	User n00c
	visualization, viewer, tview, sequence, samtools, sam, mapping, li, alignment
2009-06-09	User natstreet
	software, ngs, gbrowse, format-conversion, alignment
	User sandfire
	assembly, sanger, sequencing, software
	User druvus
	next_generation, software, standard

alignment	9
ngs	7
software	7
sequence	3
samtools	3
standard	2
format	2
sequencing	2
viewer	2
mapping	2
tool	2
assembly	2
sam	2
nextgen	2
nextgenerationsequencing	2
hts	2
next-generation-sequencing	2
sanger	1
sequencealignment	1
snp	1
method	1
seq	1
keypaper	1
short-read	1
next_generation	1
alignment-based	1
utility	1
sequences	1
li	1
high-throughput-sequencing	1
tview	1
algorithm	1
applications	1
bam	1
gbrowse	1
bioinformatics	1
add	1
visualization	1
genomic	1
short-read-mapping	1
format-conversion	1
short-reads	1
genomics	1
read-mapping	1
short_reads	1
file-format	1

The Sequence Alignment/Map format and SAMtools.

Abstract

View the full article here:

Tag Summary