Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. (3rd November 2017)

• Record Type: Journal Article
• Authors: Jayakumar, Vasanthan; Sakakibara, Yasubumi
• Is Part Of: Briefings in bioinformatics. Volume 20:Number 3(2019)
• Page Start: 866
• Page End: 876
• Publication Date: 2017-11-03
• Subjects: de novo assembly -- third-generation sequencing -- single-molecule sequencing -- PacBio SMRT -- assembly evaluation; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbx147
• Languages: English
• ISSNs: 1467-5463

Abstract

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.