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TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. / Mikheenko, Alla ; Bzikadze, Andrey; Gurevich, Alexey ; Miga, Karen; Певзнер, Павел Аркадьевич.

в: Bioinformatics, Том 36, № 1, 01.07.2020, стр. i75–i83.

Результаты исследований: Научные публикации в периодических изданиях › статья › Рецензирование

Harvard

Mikheenko, A, Bzikadze, A, Gurevich, A, Miga, K & Певзнер, ПА 2020, 'TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats', Bioinformatics, Том. 36, № 1, стр. i75–i83. https://doi.org/10.1093/bioinformatics/btaa440

APA

Mikheenko, A., Bzikadze, A., Gurevich, A., Miga, K., & Певзнер, П. А. (2020). TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics, 36(1), i75–i83. https://doi.org/10.1093/bioinformatics/btaa440

Vancouver

Mikheenko A, Bzikadze A, Gurevich A, Miga K, Певзнер ПА. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics. 2020 Июль 1;36(1):i75–i83. https://doi.org/10.1093/bioinformatics/btaa440

Author

Mikheenko, Alla ; Bzikadze, Andrey ; Gurevich, Alexey ; Miga, Karen ; Певзнер, Павел Аркадьевич. / TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. в: Bioinformatics. 2020 ; Том 36, № 1. стр. i75–i83.

BibTeX

@article{2b9804c816884cff9972edf5633e2a8c,
title = "TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats",
abstract = "MotivationExtra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.ResultsTo address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.",
author = "Alla Mikheenko and Andrey Bzikadze and Alexey Gurevich and Karen Miga and Певзнер, {Павел Аркадьевич}",
year = "2020",
month = jul,
day = "1",
doi = "10.1093/bioinformatics/btaa440",
language = "English",
volume = "36",
pages = "i75–i83",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "1",
note = "28th Conference on International Society for Computational Biology, ISMB 2020 ; Conference date: 13-07-2020 Through 16-07-2020",

}

RIS

TY - JOUR

T1 - TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

AU - Mikheenko, Alla

AU - Bzikadze, Andrey

AU - Gurevich, Alexey

AU - Miga, Karen

AU - Певзнер, Павел Аркадьевич

PY - 2020/7/1

Y1 - 2020/7/1

N2 - MotivationExtra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.ResultsTo address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.

AB - MotivationExtra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies.ResultsTo address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres.

UR - https://academic.oup.com/bioinformatics/article/36/Supplement_1/i75/5870463

UR - http://www.scopus.com/inward/record.url?scp=85087923906&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btaa440

DO - 10.1093/bioinformatics/btaa440

M3 - Article

VL - 36

SP - i75–i83

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 1

T2 - 28th Conference on International Society for Computational Biology

Y2 - 13 July 2020 through 16 July 2020

ER -

ID: 60722634