pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
| Autor: | Xiaolong Zhang, Jichao Tian, Yuwei Liao, Yanyan Shao, Peiying Li, Jun Chen, Zhiguang Li, Yu Zhang |
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| Rok vydání: | 2018 |
| Předmět: |
Computer science
Primer trimming lcsh:Computer applications to medicine. Medical informatics Biochemistry DNA sequencing Trim Deep sequencing 03 medical and health sciences 0302 clinical medicine Structural Biology Genetic variation Humans Multiplex Sensitivity (control systems) Molecular Biology Throughput (business) lcsh:QH301-705.5 030304 developmental biology 0303 health sciences business.industry Applied Mathematics High-Throughput Nucleotide Sequencing Pattern recognition Sequence Analysis DNA Computer Science Applications Multiplex amplicon sequencing lcsh:Biology (General) 030220 oncology & carcinogenesis Amplicon sequencing lcsh:R858-859.7 Trimming Artificial intelligence DNA microarray Primer (molecular biology) business Algorithms Software Target sequencing |
| Zdroj: | BMC Bioinformatics BMC Bioinformatics, Vol 20, Iss 1, Pp 1-6 (2019) |
| ISSN: | 1471-2105 |
| Popis: | 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. Electronic supplementary material The online version of this article (10.1186/s12859-019-2854-x) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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