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ARCS: Assembly Roundup by Chromium Scaffolding

Sarah Yeo, Lauren Coombe, Justin Chu, View ORCID ProfileRené L Warren, View ORCID ProfileInanç Birol
doi: https://doi.org/10.1101/100750
Sarah Yeo
BC Cancer Agency, Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
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Lauren Coombe
BC Cancer Agency, Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
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Justin Chu
BC Cancer Agency, Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
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René L Warren
BC Cancer Agency, Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
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  • For correspondence: rwarren@bcgsc.ca
Inanç Birol
BC Cancer Agency, Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
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  • ORCID record for Inanç Birol
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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

Supplementary information available online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 17, 2017.
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ARCS: Assembly Roundup by Chromium Scaffolding
Sarah Yeo, Lauren Coombe, Justin Chu, René L Warren, Inanç Birol
bioRxiv 100750; doi: https://doi.org/10.1101/100750
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ARCS: Assembly Roundup by Chromium Scaffolding
Sarah Yeo, Lauren Coombe, Justin Chu, René L Warren, Inanç Birol
bioRxiv 100750; doi: https://doi.org/10.1101/100750

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