ARCS: scaffolding genome drafts with linked reads

Bioinformatics
Sarah YeoInanc Birol

Abstract

Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA-a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics. Here, we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiens genome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data for connecting high-quality sequences in genome assembly drafts. https://github.com/bcgsc/ARCS/. rwarren@bcgsc.ca. Supplementary data are available at Bioinformatics online.

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Citations

Dec 14, 2017·Genes·Samantha J JonesSteven J M Jones
May 17, 2018·Human Molecular Genetics·Martin O PollardManjinder S Sandhu
Nov 30, 2018·Annual Review of Animal Biosciences·Jose V LopezIliana B Baums
Feb 21, 2019·Bioinformatics·Antoine LimassetPierre Peterlongo
Jun 6, 2019·PLoS Computational Biology·Jay Ghurye, Mihai Pop
Jun 30, 2019·Genes·Harwood H KwanSteven J M Jones
Jun 20, 2019·GigaScience·Qing LiZhonghua Zhang
Jun 22, 2018·BMC Bioinformatics·Lauren CoombeRene L Warren
Nov 1, 2019·BMC Bioinformatics·Junwei LuoChaokun Yan
Mar 11, 2020·Molecular Ecology Resources·Jocelyn P ColellaMatthew D MacManes
Sep 13, 2019·Bioinformatics·Ivan TolstoganovPavel A Pevzner
Nov 29, 2019·Scientific Reports·Sunnvør Í KongsstovuHans Atli Dahl
Mar 13, 2020·Scientific Data·Maria KyriakidouMartina V Strömvik
Mar 31, 2018·Nature Reviews. Genetics·Fritz J SedlazeckMichael C Schatz
Oct 28, 2018·BMC Bioinformatics·Shaun D JackmanInanc Birol
Mar 21, 2020·Genome Biology·Fatih KaraoğlanoğluCan Alkan
Nov 14, 2018·Bioinformatics·Ibrahim NumanagicFaraz Hach
Sep 30, 2020·Nature Genetics·Qian ZhouSanwen Huang
Nov 21, 2020·Bioinformatics·Markus HiltunenHanna Johannesson

Related Concepts

Clinical Protocols
DNA
Genome
Chromosome Structures
Molecular Assembly/Self Assembly
Genomics
Abyssal strain AIII3*
Nucleic Acid Sequencing
Arthrogryposis Renal Dysfunction Cholestasis Syndrome
DNA Barcode, Taxonomic

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