Nat Methods. 2009 Nov;6(11 Suppl):S6-S12. doi: 10.1038/nmeth.1376.

Sense from sequence reads: methods for alignment and assembly.

Source

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. flicek@ebi.ac.uk

Abstract

The most important first step in understanding next-generation sequencing data is the initial alignment or assembly that determines whether an experiment has succeeded and provides a first glimpse into the results. In parallel with the growth of new sequencing technologies, several algorithms that align or assemble the large data output of today's sequencing machines have been developed. We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools.

PMID:: 19844229; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Grant Support

Publication Types

MeSH Terms

Grant Support

Wellcome Trust/United Kingdom

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Analysis of high-throughput sequencing data. [Methods Mol Biol. 2011]
Analysis of high-throughput sequencing data.
Mane SP, Modise T, Sobral BW. Methods Mol Biol. 2011; 678:1-11.
Fragment assembly with short reads. [Bioinformatics. 2004]
Fragment assembly with short reads.
Chaisson M, Pevzner P, Tang H. Bioinformatics. 2004 Sep 1; 20(13):2067-74. Epub 2004 Apr 1.
Fast and accurate short read alignment with Burrows-Wheeler transform. [Bioinformatics. 2009]
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R. Bioinformatics. 2009 Jul 15; 25(14):1754-60. Epub 2009 May 18.
Review A survey of sequence alignment algorithms for next-generation sequencing. [Brief Bioinform. 2010]
Review A survey of sequence alignment algorithms for next-generation sequencing.
Li H, Homer N. Brief Bioinform. 2010 Sep; 11(5):473-83. Epub 2010 May 11.
Review Next-generation gap. [Nat Methods. 2009]
Review Next-generation gap.
McPherson JD. Nat Methods. 2009 Nov; 6(11 Suppl):S2-5.

See reviews... See all...

Cited by 50 PubMed Central articles

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. [Sci Rep. 2013]
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC. Sci Rep. 2013; 3:1512.
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. [BMC Genomics. 2013]
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.
Chen Q, Sun F. BMC Genomics. 2013; 14 Suppl 1:S1. Epub 2013 Jan 21.
Review of massively parallel DNA sequencing technologies. [Hugo J. 2011]
Review of massively parallel DNA sequencing technologies.
Moorthie S, Mattocks CJ, Wright CF. Hugo J. 2011 Dec; 5(1-4):1-12. Epub 2011 Oct 27.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Sense from sequence reads: methods for alignment and assembly.
Sense from sequence reads: methods for alignment and assembly.
Nat Methods. 2009 Nov ;6(11 Suppl):S6-S12. doi: 10.1038/nmeth.1376.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: