ARCS: Assembly Roundup by Chromium Scaffolding

BioRxiv : the Preprint Server for Biology
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 lack of linkage information over long stretches of DNA - a shortcoming that is being addressed by new sequencing protocols, such as linked reads from 10X 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 Chromium data for connecting high-quality sequences in genome assembly drafts. Availability: http://www.bcgsc.ca/platform/bioinfo/software/arcs

Related Concepts

Clinical Protocols
DNA
Genome
Computer Software
Tissue Scaffolds
Chromosome Structures
Molecular Assembly/Self Assembly
Genomics
Abyssal strain AIII3*
Nucleic Acid Sequencing

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