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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

1
McKusick-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
PMCID:
PMC3198573
DOI:
10.1093/bioinformatics/btr507
[Indexed for MEDLINE]
Free PMC Article

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