Family reunion via error correction: an efficient analysis of duplex sequencing data.

BMC Bioinformatics
Nicholas StolerAnton Nekrutenko

Abstract

Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts. This strategy comes at a cost-sequencing the same molecule multiple times increases dynamic range but significantly diminishes coverage, making whole genome duplex sequencing prohibitively expensive. Furthermore, every duplex experiment produces a substantial proportion of singleton reads that cannot be used in the analysis and are thrown away. In this paper we demonstrate that a significant fraction of these reads contains PCR or sequencing errors within duplex tags. Correction of such errors allows "reuniting" these reads with their respective families increasing the output of the method and making it more cost effective. We combine an error correction strategy with a number of algorithmic improvements in a new version of the duplex analysis software, Du Novo 2.0. It is written in Python, C, AWK, and Bash. It is open source and readily available through Galaxy, Bioconda, and Github: https://github.com/...Continue Reading

References

Mar 23, 2005·BMC Bioinformatics·Alexey LarionovWilliam Miller
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Aug 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael W SchmittLawrence A Loeb
May 6, 2014·Nature Methods·Mikhail ShugayDmitriy M Chudakov
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Boris Rebolledo-JaramilloKateryna D Makova
Apr 8, 2015·Nature Methods·Michael W SchmittLawrence A Loeb
Aug 28, 2016·Genome Biology·Nicholas StolerAnton Nekrutenko
May 6, 2017·PLoS Computational Biology·Mikhail ShugayDmitriy M Chudakov
Mar 27, 2018·Nature Reviews. Genetics·Jesse J SalkLawrence A Loeb

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Citations

Feb 13, 2021·NAR Genomics and Bioinformatics·Gundula PovysilIrene Tiemann-Boege

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Methods Mentioned

BETA
Duplex Sequencing
Illumina sequencing
PCR

Software Mentioned

py
Kalign2
Du
Bowtie2
SeqAn
MAFFT
correct
build
aligner
make

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