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 ignore the quality scores of the base calls.
“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
FLASH constructs merged reads that maximize the overlap length-to-matches ratio.
“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
FLASH requires the mean DNA fragment size and standard deviation of the fragment size as input parameters.
“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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- 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 › Computer Science › Artificial Intelligence › 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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