Research Article
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Published Online: 1 November 2017

cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing

Publication: Journal of Computational Biology
Volume 24, Issue Number 11

Abstract

Cutting of primers from reads is an important step of processing targeted amplicon-based next generation sequencing data. Existing tools are adapted for cutting of one or several primer/adapter sequences from reads and removing all of their occurrences. Also most of the existing tools use kmers and may cut only part of primers or primers with studied sequence of gene. Because of this, use of such programs leads to incorrect trimming, reduction of coverage, and increase in the number of false-positive and/or false-negative results. We have developed a new tool named cutPrimers for accurate cutting of any number of primers from reads. Using sequencing reads that were obtained during study of BRCA1/2 genes, we compared it with cutadapt, AlienTrimmer, and BBDuk. All of them trimmed reads in such a way that coverage of at least two amplicons decreased to unacceptable level (<30 reads) comparing with reads trimmed with cutPrimers. At the same time, Trimmomatic and AlienTrimmer cut all occurrences of primer sequences, so the length of the remaining reads was less than prospective.

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References

cutPrimers is freely available at https://github.com/aakechin/cutPrimers and runs under Linux, Windows, and Mac OS.
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Information & Authors

Information

Published In

cover image Journal of Computational Biology
Journal of Computational Biology
Volume 24Issue Number 11November 2017
Pages: 1138 - 1143
PubMed: 28715235

History

Published in print: November 2017
Published online: 1 November 2017
Published ahead of print: 17 July 2017

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    Authors

    Affiliations

    Andrey Kechin
    Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
    Novosibirsk State University, Novosibirsk, Russia.
    Uljana Boyarskikh
    Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
    Alexander Kel
    Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
    geneXplain GmbH, Wolfenbuettel, Germany.
    biosoft.ru, Novosibirsk, Russia.
    Maxim Filipenko
    Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.

    Notes

    Address correspondence to:Andrey KechinInstitute of Chemical Biology and Fundamental Medicine SB RASNovosibirsk 630090Russia
    E-mail: [email protected]

    Author Disclosure Statement

    The authors declare that no competing financial interests exist.

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