platanus & DBG2OLC

 

Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. 

 

 

 

 

 

 

 

 

 

参考来源：

[1]Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Genome Res. 2014 Aug;24(8):1384-95. doi: 10.1101/gr.170720.113.

https://www.ncbi.nlm.nih.gov/pubmed/24755901

[2]Ye, Chengxi, et al. "DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies." Scientific reports 6 (2016): 31900.

https://www.nature.com/articles/srep31900