Technology dictates algorithms: recent developments in read alignment

Mohammed Alser; Jeremy Rotman; Dhrithi Deshpande; Kodi Taraszka; Huwenbo Shi; Pelin Icer Baykal; Harry Taegyun Yang; Victor Xue; Sergey Knyazev; Benjamin D Singer; Brunilda Balliu; David Koslicki; Pavel Skums; Alex Zelikovsky; Can Alkan; Onur Mutlu; Serghei Mangul

doi:10.1186/s13059-021-02443-7

Technology dictates algorithms: recent developments in read alignment

Genome Biol. 2021 Aug 26;22(1):249. doi: 10.1186/s13059-021-02443-7.

Authors

Mohammed Alser^#^{1

2

3}, Jeremy Rotman^#⁴, Dhrithi Deshpande⁵, Kodi Taraszka⁴, Huwenbo Shi^{6

7}, Pelin Icer Baykal⁸, Harry Taegyun Yang^{4

9}, Victor Xue⁴, Sergey Knyazev⁸, Benjamin D Singer^{10

11

12}, Brunilda Balliu¹³, David Koslicki^{14

15

16}, Pavel Skums⁸, Alex Zelikovsky^{8

17}, Can Alkan^{2

18}, Onur Mutlu^#^{1

2

3}, Serghei Mangul^#¹⁹

Affiliations

¹ Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland.
² Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey.
³ Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland.
⁴ Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA.
⁵ Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA.
⁶ Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
⁷ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
⁸ Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA.
⁹ Bioinformatics Interdepartmental Ph.D. Program, University of California Los Angeles, Los Angeles, CA, 90095, USA.
¹⁰ Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
¹¹ Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, USA.
¹² Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
¹³ Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
¹⁴ Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16801, USA.
¹⁵ Biology Department, Pennsylvania State University, University Park, PA, 16801, USA.
¹⁶ The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16801, USA.
¹⁷ The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
¹⁸ Bilkent-Hacettepe Health Sciences and Technologies Program, Ankara, Turkey.
¹⁹ Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA. serghei.mangul@gmail.com.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Algorithms*
Computational Biology / methods*
Genome, Human
HIV / physiology
Humans
Metagenomics
Sequence Alignment*
Sulfites

Substances

Sulfites
hydrogen sulfite

Abstract

Publication types

MeSH terms

Substances

Grants and funding