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

Andrey Kechin, Uljana Boyarskikh, Alexander Kel, Maxim Filipenko

Research output: Contribution to journalArticlepeer-review

54 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1138-1143
Number of pages6
JournalJournal of Computational Biology
Issue number11
Publication statusPublished - 1 Nov 2017


  • Cutting of primer sequences
  • Next generation sequencing
  • Trimming reads


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