Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data

Vasanthan Jayakumar, Yasubumi Sakakibara

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.

Original languageEnglish
Article numberbbx147
Pages (from-to)866-876
Number of pages11
JournalBriefings in Bioinformatics
Volume20
Issue number3
DOIs
Publication statusPublished - 2017 Nov 2

Keywords

  • assembly evaluation
  • de novo assembly
  • PacBio SMRT
  • single-molecule sequencing
  • third-generation sequencing

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

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