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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
QTrim: A novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform
BMC Bioinformatics, Volume 15, No. 1, Article 33, Year 2014
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Description
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. © 2014 Shrestha et al.; licensee BioMed Central Ltd.
Authors & Co-Authors
Shrestha, Ram K.
South Africa, Bellville
University of the Western Cape
Lubinsky, Baruch
Ireland, Galway
University of Galway
Bansode, Vijay B.
Ireland, Galway
University of Galway
France, Strasbourg
Architecture et Réactivité de L'arn
Moinz, Mónica B.J.
Ireland, Galway
University of Galway
United Kingdom, Coventry
Faculty of Science, Engineering and Medicine
McCormack, Grace P.
Ireland, Galway
University of Galway
Travers, Simon A.A.
South Africa, Bellville
University of the Western Cape
Statistics
Citations: 31
Authors: 6
Affiliations: 4
Identifiers
Doi:
10.1186/1471-2105-15-33
e-ISSN:
14712105
Study Design
Cross Sectional Study