Technology dictates algorithms: recent developments in read alignment
Posted on 2021-08-27 - 03:26
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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Alser, Mohammed; Rotman, Jeremy; Deshpande, Dhrithi; Taraszka, Kodi; Shi, Huwenbo; Baykal, Pelin Icer; et al. (2021). Technology dictates algorithms: recent developments in read alignment. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.5585907.v1
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AUTHORS (17)
MA
Mohammed Alser
JR
Jeremy Rotman
DD
Dhrithi Deshpande
KT
Kodi Taraszka
HS
Huwenbo Shi
PB
Pelin Icer Baykal
HY
Harry Taegyun Yang
VX
Victor Xue
SK
Sergey Knyazev
BS
Benjamin D. Singer
BB
Brunilda Balliu
DK
David Koslicki
PS
Pavel Skums
AZ
Alex Zelikovsky
CA
Can Alkan
OM
Onur Mutlu
SM
Serghei Mangul