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QTrim : a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform
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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.
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Official URL: http://dx.doi.org/10.1186/1471-2105-15-33
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: |
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| 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) |
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