pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
Abstract Background With the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream analysis. Although some tools are currently available, their efficiency...
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doaj-233416a888c54152be5b22fca66db17d2020-11-25T03:07:27ZengBMCBMC Bioinformatics1471-21052019-05-012011610.1186/s12859-019-2854-xpTrimmer: An efficient tool to trim primers of multiplex deep sequencing dataXiaolong Zhang0Yanyan Shao1Jichao Tian2Yuwei Liao3Peiying Li4Yu Zhang5Jun Chen6Zhiguang Li7Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityThe Second Hospital of Dalian Medical UniversityCenter of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical UniversityAbstract Background With the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream analysis. Although some tools are currently available, their efficiency and accuracy require improvement in trimming large scale of primers in high throughput target genome sequencing. This issue is becoming more urgent considering the potential clinical implementation of MAS for processing patient samples. We here developed pTrimmer that could handle thousands of primers simultaneously with greatly improved accuracy and performance. Result pTrimmer combines the two algorithms of k-mers and Needleman-Wunsch algorithm, which ensures its accuracy even with the presence of sequencing errors. pTrimmer has an improvement of 28.59% sensitivity and 11.87% accuracy compared to the similar tools. The simulation showed pTrimmer has an ultra-high sensitivity rate of 99.96% and accuracy of 97.38% compared to cutPrimers (70.85% sensitivity rate and 58.73% accuracy). And the performance of pTrimmer is notably higher. It is about 370 times faster than cutPrimers and even 17,000 times faster than cutadapt per threads. Trimming 2158 pairs of primers from 11 million reads (Illumina PE 150 bp) takes only 37 s and no more than 100 MB of memory consumption. Conclusions pTrimmer is designed to trim primer sequence from multiplex amplicon sequencing and target sequencing. It is highly sensitive and specific compared to other three similar tools, which could help users to get more reliable mutational information for downstream analysis.http://link.springer.com/article/10.1186/s12859-019-2854-xPrimer trimmingTarget sequencingMultiplex amplicon sequencing |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiaolong Zhang Yanyan Shao Jichao Tian Yuwei Liao Peiying Li Yu Zhang Jun Chen Zhiguang Li |
spellingShingle |
Xiaolong Zhang Yanyan Shao Jichao Tian Yuwei Liao Peiying Li Yu Zhang Jun Chen Zhiguang Li pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data BMC Bioinformatics Primer trimming Target sequencing Multiplex amplicon sequencing |
author_facet |
Xiaolong Zhang Yanyan Shao Jichao Tian Yuwei Liao Peiying Li Yu Zhang Jun Chen Zhiguang Li |
author_sort |
Xiaolong Zhang |
title |
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data |
title_short |
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data |
title_full |
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data |
title_fullStr |
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data |
title_full_unstemmed |
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data |
title_sort |
ptrimmer: an efficient tool to trim primers of multiplex deep sequencing data |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-05-01 |
description |
Abstract Background With the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream analysis. Although some tools are currently available, their efficiency and accuracy require improvement in trimming large scale of primers in high throughput target genome sequencing. This issue is becoming more urgent considering the potential clinical implementation of MAS for processing patient samples. We here developed pTrimmer that could handle thousands of primers simultaneously with greatly improved accuracy and performance. Result pTrimmer combines the two algorithms of k-mers and Needleman-Wunsch algorithm, which ensures its accuracy even with the presence of sequencing errors. pTrimmer has an improvement of 28.59% sensitivity and 11.87% accuracy compared to the similar tools. The simulation showed pTrimmer has an ultra-high sensitivity rate of 99.96% and accuracy of 97.38% compared to cutPrimers (70.85% sensitivity rate and 58.73% accuracy). And the performance of pTrimmer is notably higher. It is about 370 times faster than cutPrimers and even 17,000 times faster than cutadapt per threads. Trimming 2158 pairs of primers from 11 million reads (Illumina PE 150 bp) takes only 37 s and no more than 100 MB of memory consumption. Conclusions pTrimmer is designed to trim primer sequence from multiplex amplicon sequencing and target sequencing. It is highly sensitive and specific compared to other three similar tools, which could help users to get more reliable mutational information for downstream analysis. |
topic |
Primer trimming Target sequencing Multiplex amplicon sequencing |
url |
http://link.springer.com/article/10.1186/s12859-019-2854-x |
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