fqtools: An efficient software suite for modern FASTQ file manipulation

Abstract

Summary: Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (for example searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.

Metadata

Authors/Creators:	Droop, AP
Copyright, Publisher and Additional Information:	© The Author(s) 2016. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords:	Next-generation sequencing; Sequence analysis; Programming; Bioinformatics
Dates:	Accepted: 11 February 2016 Published (online): 18 February 2016 Published: 15 June 2016
Institution:	The University of Leeds
Academic Units:	The University of Leeds > Faculty of Medicine and Health (Leeds)
Depositing User:	Symplectic Publications
Date Deposited:	02 Mar 2016 12:44
Last Modified:	11 Apr 2018 15:44
Published Version:	http://dx.doi.org/10.1093/bioinformatics/btw088
Status:	Published
Publisher:	Oxford University Press
Identification Number:	https://doi.org/10.1093/bioinformatics/btw088

CORE (COnnecting REpositories)

fqtools: An efficient software suite for modern FASTQ file manipulation

Abstract

Metadata

Download

Published Version

Export

Statistics