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Cited by 144Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

Technology dictates algorithms: recent developments in read alignment

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Alser, Mohammed, Rotman, Jeremy, Deshpande, Dhrithi, Taraszka, Kodi, Shi, Huwenbo, Baykal, Pelin Icer, Yang, Harry Taegyun, Xue, Victor +9 more·2021·Genome Biology
DOI 10.1186/s13059-021-02443-7PMC PMC8390189
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Abstract

Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today’s diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.

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  • Exact methods, including those based on dynamic programming, are often used for refining alignments or for aligning smaller regions of the genome.

    “Such methods, including those based on dynamic programming, are often used for refining alignments or for aligning smaller regions of the genome [60,61].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [61]

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Authors
Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., Balliu, B., Koslicki, D., Skums, P., Zelikovsky, A., Alkan, C., Mutlu, O., & Mangul, S.
Affiliations
  • Bilkent University (TR)
  • University of California, Los Angeles (US)
  • University of Southern California (US)
  • Broad Institute (US)
  • Georgia State University (US)
  • Northwestern University (US)
  • Pennsylvania State University (US)
  • Sechenov University (RU)
Corresponding author
Mangul, Serghei
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2021-08-26
Volume
22
Issue
1
Pages
249-249
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-021-02443-7
PMC
PMC8390189
OpenAlex
W3008701988
Cited by
144
References
13
Citations by year
2026: 24 · 2025: 25 · 2024: 37 · 2023: 29 · 2022: 20 · 2021: 5 · 2020: 3 · 2012: 1
FWCI
2.42
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
  • arXiv (Cornell University)
  • ETH Zürich Research Collection (cc-by)
  • Figshare (cc-by)
Funders
  • National Heart, Lung, and Blood Institute (K08HL128867)
  • National Institutes of Health (1R01EB025022, R01HL149883, R01HL153122, HG006004)
  • National Science Foundation (2047828, 2041984)
  • Molecular Basis of Disease
  • Intel Corporation
  • VMware
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
read mapping, sequence alignment algorithms, short-read sequencing, long-read sequencing, reference genome mapping
MeSH terms
Algorithms, HIV, Humans, Sulfites, Genome, Human, Sequence Alignment, Computational Biology, Metagenomics

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