The Sequence Alignment/Map format and SAMtools

Bioinformatics - Tập 25 Số 16 - Trang 2078-2079 - 2009
Heng Li1, Robert E. Handsaker1, Alec Wysoker1, Tim Fennell1, Jue Ruan1, Nils Homer1, Gábor Marth1, Gonçalo R. Abecasis1, Richard Durbin1
11 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, 2Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA, 3Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China, 4Department of Computer Science, University of California Los Angeles, Los Angeles, CA 90095, 5Department of Biology, Boston College, Chestnut Hill, MA 02467, 6Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA and 7http://1000genomes.org

Tóm tắt

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

Contact:  [email protected]

Từ khóa


Tài liệu tham khảo

Kent, 2002, The human genome browser at UCSC, Genome Res., 12, 996, 10.1101/gr.229102

Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25

Li, 2008, Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Res., 18, 1851, 10.1101/gr.078212.108

Mardis, 2008, Next-generation DNA sequencing methods, Annu. Rev. Genomics Hum. Genet., 9, 387, 10.1146/annurev.genom.9.081307.164359

Thông tin
Thông tin xuất bản

Bioinformatics

Tập 25 Số 16

2078-2079

Thông tin tác giả