Research Article
No access
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


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.

Get full access to this article

View all available purchase options and get full access to this article.


cutPrimers is freely available at and runs under Linux, Windows, and Mac OS.
Betge J., Kerr G., Miersch T., et al. 2015. Amplicon sequencing of colorectal cancer: Variant calling in frozen and formalin-fixed samples. PLoS One 10, e0127146.
Bolger A.M., Lohse M., and Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
Cock P.J.A., Antao T., Chang J.T., et al. 2009. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422–1423.
Criscuolo A., and Brisse S. 2013. AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics 102, 500–506.
Ermolenko N.A., Boyarskikh U.A., Kechin A.A., et al. 2015. Massive parallel sequencing for diagnostic genetic testing of BRCA genes—A single center experience. Asian Pac. J. Cancer Prev. 16, 7935–7941.
Li H., and Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760.
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10.
Nguyen-Dumont T., Pope B.J., Hammet F., et al. 2013. A high-plex PCR approach for massively parallel sequencing. Biotechniques 55, 69–74.
Yan B., Hu Y., Ng C., et al. 2016. Coverage analysis in a targeted amplicon-based next-generation sequencing panel for myeloid neoplasms. J. Clin. Pathol. 69, 801–804.

Information & Authors


Published In

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


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


Request permissions for this article.




    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., Novosibirsk, Russia.
    Maxim Filipenko
    Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.


    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.

    Metrics & Citations



    Export citation

    Select the format you want to export the citations of this publication.

    View Options

    Get Access

    Access content

    To read the fulltext, please use one of the options below to sign in or purchase access.

    Society Access

    If you are a member of a society that has access to this content please log in via your society website and then return to this publication.

    Restore your content access

    Enter your email address to restore your content access:

    Note: This functionality works only for purchases done as a guest. If you already have an account, log in to access the content to which you are entitled.

    View options


    View PDF/ePub

    Full Text

    View Full Text







    Copy the content Link

    Share on social media

    Back to Top