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.

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。