Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Nov 1;27(21):2957-63. doi: 10.1093/bioinformatics/btr507. Epub 2011 Sep 7.

FLASH: fast length adjustment of short reads to improve genome assemblies.

Author information

  • 1McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. t.magoc@gmail.com

Abstract

MOTIVATION:

Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.

RESULTS:

We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.

AVAILABILITY AND IMPLEMENTATION:

The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.

CONTACT:

t.magoc@gmail.com.

PMID:
21903629
[PubMed - indexed for MEDLINE]
PMCID:
PMC3198573
Free PMC Article

Images from this publication.See all images (7)Free text

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.
Fig. 7.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk