PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes. (April 2020)

• Record Type: Journal Article
• Authors: Lu, Peng; Jin, Jingjing; Li, Zefeng; Xu, Yalong; Hu, Dasha; Liu, Jiajun; Cao, Peijian
• Is Part Of: Evolutionary bioinformatics online. Volume 16(2020)
• Publication Date: 2020-04
• Subjects: Parallel -- long-reads -- gap-closing; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.1177/1176934320913859
• Languages: English
• ISSNs: 1176-9343

Abstract

Assembled draft genomes usually contain many gaps because of the length limit of next-generation sequencing. Although many gap-closing tools have been developed, most of them still attempt to fill gaps on the basis of next-generation sequencing reads (always < 200 bp). Hence, the gap-filling effect is inferior. Several tools that use long-reads to close gaps have recently been created. However, they require extensive runtimes, which may not be suitable for large genomes. We describe a gap-closing tool called PGcloser, which supports parallel mode and adopts long-reads/contigs to fill gaps in genome sequences. Three tests show that PGcloser is faster than other tools but exhibits similar accuracy. PGcloser is free open-source software that is available athttp://software.tobaccodb.org/software/pgcloser .