Skip to content Skip to navigation
University of Warwick
  • Study
  • |
  • Research
  • |
  • Business
  • |
  • Alumni
  • |
  • News
  • |
  • About

University of Warwick
Publications service & WRAP

Highlight your research

  • WRAP
    • Home
    • Search WRAP
    • Browse by Warwick Author
    • Browse WRAP by Year
    • Browse WRAP by Subject
    • Browse WRAP by Department
    • Browse WRAP by Funder
    • Browse Theses by Department
  • Publications Service
    • Home
    • Search Publications Service
    • Browse by Warwick Author
    • Browse Publications service by Year
    • Browse Publications service by Subject
    • Browse Publications service by Department
    • Browse Publications service by Funder
  • Help & Advice
University of Warwick

The Library

  • Login
  • Admin

QTrim : a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform

Tools
- Tools
+ Tools

Shrestha, Ram, Lubinsky, Baruch, Bansode, Vijay B., Moinz, Mónica B. J., McCormack, Grace P. and Travers, Simon A. (2014) QTrim : a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform. BMC Bioinformatics, Volume 15 (Number 1). Article number 33. doi:10.1186/1471-2105-15-33 ISSN 1471-2105.

[img]
Preview
PDF
WRAP_art%3A10.1186%2F1471-2105-15-33.pdf - Published Version - Requires a PDF viewer.
Available under License Creative Commons Attribution 2.0..

Download (453Kb) | Preview
Official URL: http://dx.doi.org/10.1186/1471-2105-15-33

Request Changes to record.

Abstract

Background
Many high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a sequence read. Undertaking quality trimming of this data is essential to enable confidence in the results of subsequent downstream analysis. Here, we have developed a novel, highly sensitive and accurate approach (QTrim) for the quality trimming of sequence reads generated using the Roche/454 sequencing platform (or any platform with long reads that outputs Phred-like quality scores).

Results
The performance of QTrim was evaluated against all other available quality trimming approaches on both poor and high quality 454 sequence data. In all cases, QTrim appears to perform equally as well as the best other approach (PRINSEQ) with these two methods significantly outperforming all other methods. Further analysis of the trimmed data revealed that the novel trimming approach implemented in QTrim ensures that the prevalence of low quality bases in the resulting trimmed data is substantially lower than PRINSEQ or any of the other approaches tested.

Conclusions
QTrim is a novel, highly sensitive and accurate algorithm for the quality trimming of Roche/454 sequence reads. It is implemented both as an executable program that can be integrated with standalone sequence analysis pipelines and as a web-based application to enable individuals with little or no bioinformatics experience to quality trim their sequence data.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Nucleotide sequence -- Data processing, Genomics -- Data processing
Journal or Publication Title: BMC Bioinformatics
Publisher: BioMed Central Ltd.
ISSN: 1471-2105
Official Date: January 2014
Dates:
DateEvent
January 2014Published
Volume: Volume 15
Number: Number 1
Article Number: Article number 33
DOI: 10.1186/1471-2105-15-33
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 27 December 2015
Date of first compliant Open Access: 27 December 2015
Funder: Atlantic Philanthropies (Organization), South Africa. Department of Science and Technology, Science Foundation Ireland (SFI), Marine Institute (Galway, Ireland)
Grant number: 62302 (AP), 07/RFP/ EEEOBF424 (SFI)

Request changes or add full text files to a record

Repository staff actions (login required)

View Item View Item

Downloads

Downloads per month over past year

View more statistics

twitter

Email us: wrap@warwick.ac.uk
Contact Details
About Us