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FLASH: fast length adjustment of short reads to improve genome assemblies
Open accessAbstract
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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“Both, Shera and FLASH (see later in the text) ignore the quality scores of the base calls.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Magoč and Salzberg, 2011
In the citing paper
“FLASH constructs merged reads that maximize the overlap length-to-matches ratio.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Magoč and Salzberg, 2011
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“FLASH requires the mean DNA fragment size and standard deviation of the fragment size as input parameters.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Magoč and Salzberg, 2011
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“Anyincreaseinreadlength willhaveasignificant,positiveimpactonthequalityofgenome assemblies. library of DNAfragments.”
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PEAR: a fast and accurate Illumina Paired-End reAd mergeR
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Metadata
- 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
- 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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