Versatile genome assembly evaluation with QUAST-LG

Результат исследований: Научные публикации в периодических изданияхстатья

45 Цитирования (Scopus)

Аннотация

Motivation: The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. Results: In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG?a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference.

Язык оригиналаанглийский
Страницы (с-по)i142-i150
ЖурналBioinformatics
Том34
Номер выпуска13
DOI
СостояниеОпубликовано - 1 июл 2018
Опубликовано для внешнего пользованияДа
СобытиеIntelligent Systems for Molecular Biology - Чикаго, Соединенные Штаты Америки
Продолжительность: 6 июл 201810 июл 2018
Номер конференции: 2018
https://www.iscb.org/ismb2018

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Предметные области Scopus

  • Теория вероятности и статистика
  • Биохимия
  • Молекулярная биология
  • Прикладные компьютерные науки
  • Математика и теория расчета
  • Вычислительная математика

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