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PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes
Evolutionary Bioinformatics ( IF 1.7 ) Pub Date : 2020-04-23 , DOI: 10.1177/1176934320913859
Peng Lu 1 , Jingjing Jin 1 , Zefeng Li 1 , Yalong Xu 1 , Dasha Hu 2 , Jiajun Liu 2 , Peijian Cao 1
Affiliation  

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 at http://software.tobaccodb.org/software/pgcloser.



中文翻译:

PGcloser:使用长读数或重叠群填补基因组缺口的快速平行缺口封闭工具

由于下一代测序的长度限制,组装的草图基因组通常包含许多缺口。尽管已经开发出许多封闭缺口的工具,但它们中的大多数仍试图在下一代测序读数(始终<200 bp)的基础上填补空白。因此,间隙填充效果较差。最近已经创建了一些使用长读来填补空白的工具。但是,它们需要大量的运行时,可能不适用于大型基因组。我们描述了一种称为PGcloser的缺口闭合工具,该工具支持并行模式,并采用长读/重叠序列来填补基因组序列中的缺口。三个测试表明PGcloser比其他工具快,但显示出相似的精度。PGcloser是免费的开源软件,可从http://software.tobaccodb.org/software/pgcloser获得。

更新日期:2020-06-30
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