skip to main content
Language:
Search Limited to: Search Limited to: Resource type Show Results with: Show Results with: Search type Index

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

Journal of computational biology, 2017-11, Vol.24 (11), p.1138-1143 [Peer Reviewed Journal]

ISSN: 1557-8666 ;EISSN: 1557-8666 ;DOI: 10.1089/cmb.2017.0096 ;PMID: 28715235

Full text available

Citations Cited by
  • Title:
    cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
  • Author: Kechin, Andrey ; Boyarskikh, Uljana ; Kel, Alexander ; Filipenko, Maxim
  • Subjects: BRCA1 Protein - genetics ; BRCA2 Protein - genetics ; Computational Biology - methods ; DNA Primers - chemistry ; DNA Primers - genetics ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Sequence Analysis, DNA - methods ; Software
  • Is Part Of: Journal of computational biology, 2017-11, Vol.24 (11), p.1138-1143
  • Description: 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.
  • Publisher: United States
  • Language: English
  • Identifier: ISSN: 1557-8666
    EISSN: 1557-8666
    DOI: 10.1089/cmb.2017.0096
    PMID: 28715235
  • Source: MEDLINE
    Alma/SFX Local Collection
Back to results list
INSPIRE LIBRARY - TON DUC THANG UNIVERSITY (84-028) 37 755 057 Feedback
19 Nguyen Huu Tho St. Dist.7, HCM thuvien@tdtu.edu.vn

Copyright © 2017 INSPIRE LIBRARY - TON DUC THANG UNIVERSITY

Searching Remote Databases, Please Wait