Cited by 15,366Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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

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Magoč, Tanja, Salzberg, Steven L.·2011·Bioinformatics

DOI 10.1093/bioinformatics/btr507PMC PMC3198573

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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.

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Authors: Magoč, T., & Salzberg, S. L.
Affiliations: Johns Hopkins University (US)
Corresponding author: Magoč, Tanja
ORCID: Salzberg, Steven L.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2011-09-07
Volume: 27
Issue: 21
Pages: 2957-2963
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btr507
PMC: PMC3198573
OpenAlex: W2157107905
Cited by: 15,366
References: 10
Citations by year: 2026: 1179 · 2025: 1544 · 2024: 1692 · 2023: 1732 · 2022: 2072 · 2021: 1845 · 2020: 1613 · 2019: 1187 · 2018: 1004 · 2017: 681 · 2016: 450 · 2015: 228 · 2014: 84 · 2013: 35 · 2012: 8
FWCI: 16.60
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Bioinformatics (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Human Genome Research Institute (R01HG006102, R01HG006677)
National Institute of General Medical Sciences (R01GM083873)
U.S. National Library of Medicine (R01LM006845)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords: Adobe Flash, paired-end reads, read merging, de novo genome assembly, fragment libraries, Staphylococcus aureus, chromosome 14
MeSH terms: Chromosomes, Human, Pair 14, Humans, Software, Staphylococcus aureus, Genome, Sequence Analysis, DNA, Genomics

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