Assembly of large genomes using second-generation sequencing

Schatz, M. C., Delcher, A. L., Salzberg, S. L. (2010) Assembly of large genomes using second-generation sequencing. Genome Research, 20 (9). pp. 1165-1173. ISSN 10889051 (ISSN)

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DOI: 10.1101/gr.101360.109


Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data. We also review the genomes that have been assembled recently from short reads and make recommendations for sequencing strategies that will yield a high-quality assembly. © 2010 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: contig DNA Atlantic cod biomedical technology assessment cost control gene sequence human human genome nonhuman priority journal review strawberry turkey bird Algorithms Base Sequence Genome, Human Genomics Humans Sequence Analysis DNA
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > computational biology
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: CSHL Librarian
Date: 2010
Date Deposited: 16 Mar 2012 13:47
Last Modified: 15 Mar 2013 19:00
PMCID: PMC2928494
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