BBMerge - Accurate paired shotgun read merging via overlap

PloS One
Brian BushnellEsther Singer

Abstract

Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highly sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information...Continue Reading

References

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Citations

Apr 18, 2018·American Journal of Botany·Matthew B ParksAndrew J Alverson
Aug 30, 2018·The ISME Journal·S E RuffA Boetius
Feb 12, 2019·The ISME Journal·Jamie W BeckerSallie W Chisholm
May 12, 2019·Molecular Biology and Evolution·Eddie K H HoSarah Schaack
Dec 4, 2019·Annals of Neurology·Erik TilchKonrad Oexle
Jan 7, 2020·Science Advances·Danielle L RudlerAleksandra Filipovska
Jan 17, 2020·Molecular Ecology Resources·Eleonora RachtmanSiavash Mirarab
Feb 28, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Charlotte H ColesStephen Harper
Feb 15, 2020·Microbiology Resource Announcements·Shenwei ZhangJan-Peter van Pijkeren
Jun 20, 2020·Current Protocols in Bioinformatics·Andrey PrjibelskiAnton Korobeynikov
Jul 14, 2020·Molecular Systems Biology·Hsing-I HoHarris H Wang
Jun 25, 2020·Journal of Cell Science·Richard G LeeAleksandra Filipovska
Aug 10, 2018·BMC Bioinformatics·Renato Renison Moreira OliveiraRonnie Alves
Mar 4, 2020·Nature Ecology & Evolution·Pauline HessenauerChristian R Landry
Sep 23, 2020·Scientific Reports·Christoph WeiseAlexander Weng
Jun 4, 2018·Microbial Ecology·Pedro J TorresAnna Edlund
Jan 6, 2019·The ISME Journal·Adrian-Ştefan AndreiRohit Ghai
Sep 5, 2019·Viruses·Matheus A DuarteFabrício S Campos

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Software Mentioned

RSEM
PEAR
BBMerge
RandomReads
Eloper
QUAST
XORRO
Reformat
leeHom
USEARCH

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