1:网页链接：

https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage

2:参考文献：

Seo J S, Rhie A, Kim J, et al. De novo assembly and phasing of a Korean human genome[J]. Nature, 2016, 538(7624): 243-7.

Bickhart D M, Rosen B D, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome[J]. Nature genetics, 2017, 49(4): 643.

Tørresen O K, Star B, Jentoft S, et al. An improved genome assembly uncovers prolific tandem repeats in Atlantic cod[J]. BMC genomics, 2017, 18(1): 95.

Walker B J, Abeel T, Shea T, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement[J]. PloS one, 2014, 9(11): e112963.

 Lok S, Paton T A, Wang Z, et al. De novo genome and transcriptome assembly of the Canadian beaver (Castor canadensis)[J]. G3: Genes, Genomes, Genetics, 2017, 7(2): 755-773.

3:参数设置参考链接：https://github.com/skoren/PilonGrid/blob/master/pilonParallelSGE.sh

4：-Xmx16G内存越大越好一般是1G内存对应1M基因组