The hidden perils of read mapping as a quality assessment tool in genome sequencing

Lehri, B., Seddon, A. M. and Karlyshev, A. V. (2017) The hidden perils of read mapping as a quality assessment tool in genome sequencing. Scientific Reports, 7(43149), ISSN (online) 2045-2322

Full text available as:
[img] Text
Lehri-B-37659-VoR.pdf - Published Version
Available under License Creative Commons Attribution.

Download (2MB)

Abstract

This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are presented using a recently completed sequence of the genome of Lactobacillus fermentum 3872. In particular, quality of assemblies is assessed by using CLC Genomics Workbench read mapping and Optical mapping developed by OpGen. Over-extension of contigs without prior knowledge of contig location can lead to misassembled contigs, even when commonly used quality indicators such as read mapping suggest that a contig is well assembled. Precautions must also be undertaken when using long read sequencing technology, which may also lead to misassembled contigs.

Item Type: Article
Research Area: Allied health professions and studies
Biological sciences
Infection and immunology
Faculty, School or Research Centre: Faculty of Science, Engineering and Computing > School of Life Sciences
Depositing User: Andrey Karlyshev
Date Deposited: 08 Mar 2017 11:31
Last Modified: 10 Apr 2017 12:50
URI: http://eprints.kingston.ac.uk/id/eprint/37659

Actions (Repository Editors)

Item Control Page Item Control Page