ARCS: Scaffolding Genome Drafts with Linked-Reads

Posted By: shauna-10x, on Oct 25, 2017 at 11:01 AM
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Linked-Reads provide long range genomic information from short reads, enabling cost-effective and straightforward de novo assembly. In a new Bioinformatics publication, Yeo, et al., present ARCS, the Assembly Round-up by Chromium Scaffolding algorithm.  ARCS utilizes Linked-Read barcoding information to further organize draft genomes into highly contiguous assemblies.

 

ABSTRACT

Motivation

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 10x Genomics.

 

Results

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.

 

ARCS on Github: https://github.com/bcgsc/ARCS/

 

Read the full article here: https://academic.oup.com/bioinformatics/article/4562503/ARCS-Scaffolding-Genome-Drafts-with-Linked-R...

 

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