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A survey of sequence alignment algorithms for next-generation sequencing
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Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central challenge to the analysis of this data is sequence alignment, whereby sequence reads must be compared to a reference. A wide variety of alignment algorithms and software have been subsequently developed over the past two years. In this article, we will systematically review the current development of these algorithms and introduce their practical applications on different types of experimental data. We come to the conclusion that short-read alignment is no longer the bottleneck of data analyses. We also consider future development of alignment algorithms with respect to emerging long sequence reads and the prospect of cloud computing.
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“When we examined the inter-site DEG false positive rates for several other analysis pipelines (WHAM34, Mapsplice35, Novoalign36, Cufflinks23, 37, 38 and HTSeq39) we found similarly high false positive rates, regardless of the analysis pipeline or read alignment methods used (Supplementary Fig. 1).”
From Detecting and correcting systematic variation in large-scale RNA sequencing data (2014) · cites this paper as [36]
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Metadata
- Authors
- Li, H., & Homer, N.
- Affiliations
- Broad Institute (US)
- ORCID
- Li, H.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-05-11
- Volume
- 11
- Issue
- 5
- Pages
- 473-483
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC2943993
- OpenAlex
- W2093931624
- Cited by
- 875
- References
- 74
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 22 · 2023: 21 · 2022: 20 · 2021: 37 · 2020: 41 · 2019: 41 · 2018: 69 · 2017: 52 · 2016: 74 · 2015: 88 · 2014: 118 · 2013: 105 · 2012: 83
- FWCI
- 7.25
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Briefings in Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U01HG005210, U01HG005208)
- 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
- sequence alignment, next-generation sequencing, short-read alignment, long-read sequencing, alignment algorithms, reference genome mapping, cloud computing, bioinformatics software
- MeSH terms
- Algorithms, Base Sequence, Humans, Software, Genome, Human, Sequence Alignment, Sequence Analysis, DNA
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