Scaffolding and completing genome assemblies in real-time with nanopore sequencing.

Abstract:

:Third generation sequencing technologies provide the opportunity to improve genome assemblies by generating long reads spanning most repeat sequences. However, current analysis methods require substantial amounts of sequence data and computational resources to overcome the high error rates. Furthermore, they can only perform analysis after sequencing has completed, resulting in either over-sequencing, or in a low quality assembly due to under-sequencing. Here we present npScarf, which can scaffold and complete short read assemblies while the long read sequencing run is in progress. It reports assembly metrics in real-time so the sequencing run can be terminated once an assembly of sufficient quality is obtained. In assembling four bacterial and one eukaryotic genomes, we show that npScarf can construct more complete and accurate assemblies while requiring less sequencing data and computational resources than existing methods. Our approach offers a time- and resource-effective strategy for completing short read assemblies.

journal_name

Nat Commun

journal_title

Nature communications

authors

Cao MD,Nguyen SH,Ganesamoorthy D,Elliott AG,Cooper MA,Coin LJ

doi

10.1038/ncomms14515

subject

Has Abstract

pub_date

2017-02-20 00:00:00

pages

14515

issn

2041-1723

pii

ncomms14515

journal_volume

8

pub_type

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