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CutPrimers : A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. / Kechin, Andrey; Boyarskikh, Uljana; Kel, Alexander et al.

In: Journal of Computational Biology, Vol. 24, No. 11, 01.11.2017, p. 1138-1143.

Research output: Contribution to journal › Article › peer-review

Harvard

Kechin, A, Boyarskikh, U, Kel, A & Filipenko, M 2017, 'CutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing', Journal of Computational Biology, vol. 24, no. 11, pp. 1138-1143. https://doi.org/10.1089/cmb.2017.0096

APA

Kechin, A., Boyarskikh, U., Kel, A., & Filipenko, M. (2017). CutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. Journal of Computational Biology, 24(11), 1138-1143. https://doi.org/10.1089/cmb.2017.0096

Vancouver

Kechin A, Boyarskikh U, Kel A, Filipenko M. CutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. Journal of Computational Biology. 2017 Nov 1;24(11):1138-1143. doi: 10.1089/cmb.2017.0096

Author

Kechin, Andrey ; Boyarskikh, Uljana ; Kel, Alexander et al. / CutPrimers : A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. In: Journal of Computational Biology. 2017 ; Vol. 24, No. 11. pp. 1138-1143.

BibTeX

@article{88f4d3255f094fb08ff20dc1eb1f7ee7,
title = "CutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing",
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.",
keywords = "Cutting of primer sequences, Next generation sequencing, Trimming reads",
author = "Andrey Kechin and Uljana Boyarskikh and Alexander Kel and Maxim Filipenko",
year = "2017",
month = nov,
day = "1",
doi = "10.1089/cmb.2017.0096",
language = "English",
volume = "24",
pages = "1138--1143",
journal = "Journal of Computational Biology",
issn = "1066-5277",
publisher = "Mary Ann Liebert Inc.",
number = "11",

}

RIS

TY - JOUR

T1 - CutPrimers

T2 - A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing

AU - Kechin, Andrey

AU - Boyarskikh, Uljana

AU - Kel, Alexander

AU - Filipenko, Maxim

PY - 2017/11/1

Y1 - 2017/11/1

N2 - 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.

AB - 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.

KW - Cutting of primer sequences

KW - Next generation sequencing

KW - Trimming reads

UR - http://www.scopus.com/inward/record.url?scp=85033370770&partnerID=8YFLogxK

U2 - 10.1089/cmb.2017.0096

DO - 10.1089/cmb.2017.0096

M3 - Article

C2 - 28715235

AN - SCOPUS:85033370770

VL - 24

SP - 1138

EP - 1143

JO - Journal of Computational Biology

JF - Journal of Computational Biology

SN - 1066-5277

IS - 11

ER -

ID: 9699511