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Статья в периодическом издании

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome

WoS 3.730/Q2 SCOPUS 2.110/Q1
DOI 10.1186/s12864-018-4475-6
Язык Английский
Журнал BMC Genomics

ISSN: 1471-2164; Онлайн ISSN: –
Год 2018
Выходные данные Том: 19, 3, Статья: 92, Страниц (электронный ресурс): 11
Авторы
  1. Naumenko F. M.
    Novosibirsk State University, Novosibirsk, Russia (ru)
  2. Abnizova I. I.
    Wellcome Trust Sanger Institute, Cambridge, UK (gbr)
    Babraham Institute, Cambridge, UK (gbr)
  3. Beka N.
    University of Hertfordshire, Hertfordshire, UK (gbr)
  4. Genaev M. A.
    Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia (ru)
  5. Орлов Ю. Л.
    Novosibirsk State University, Novosibirsk, Russia (ru)
    Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia (ru)
    ФИЦ «Институт биологии южных морей имени А. О. Ковалевского РАН»
Даты Опубликована: 09.02.2018
Абстракт Background The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome. Results We investigated whether a single chromosome mapping causes any artefacts in the alignments’ performances. In this paper, we compared the accuracy of the performance of seven aligners on well-controlled simulated benchmark data which was sampled from a single chromosome and also from a whole genome. We found that commonly used statistical methods are insufficient to evaluate an aligner performance, and applied a novel measure of a read density distribution similarity, which allowed to reveal artefacts in aligners’ performances. We also calculated some interesting mismatch statistics, and constructed mismatch frequency distributions along the read. Conclusions The generation of artificial data by mapping of reads generated from a single chromosome to a reference chromosome is justified from the point of view of reducing the benchmarking time. The proposed quality assessment method allows to identify the inherent shortcoming of aligners that are not detected by conventional statistical methods, and can affect the quality of alignment of real data.
Ключевые слова: next-generation sequencing, DNA alignment, read density distribution
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836841/

Запись создана: 10-05-2020 08:47
Последнее изменение: 20-07-2020 13:15

Текущий статус журнала
BMC Genomics
ISSN: 1471-2164
WoS: Q2

SCOPUS: Q1

Страница журнала в E-library
Библиографическая ссылка:
Naumenko F. M., Abnizova I. I., Beka N., Genaev M. A., Orlov Yu. L. Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome // BMC Genomics. 2018. Vol. 19, suppl. 3. Article no. 92 (11 p.). DOI: 10.1186/s12864-018-4475-6
[WoS 3.730/Q2][SCOPUS 2.110/Q1]
Экспертное заключение: –
Индексация на момент включения в базу:
Web of Science
Статус
Да
Импакт-фактор/Квартиль(год)
3.730/Q2 (2017)
Идентификатор
000424782900010
SCOPUS
Статус
Да
Импакт-фактор/Квартиль(год)
2.110/Q1 (2018)
Идентификатор
2-s2.0-85041837055
РИНЦ
Статус
Нет
Идентификатор
35502105