Incorporating paired end information in assemblies

[voutcn]

Incorporating paired end information in assemblies

[tseemann]

@shaman-narayanasamy If you have MiSeq or NextSeq reads, the often overlap because of a small fragment size. If you use PEAR to first overlap your reads, then give them to megahit, this will improve your assemblies a lot.

[shaman-narayanasamy]

@tseemann, thanks for the tip. Unfortunately, my reads are from HiSeq. However, I will still give it a go and assess the performance.

[tseemann]

@shaman-narayanasamy The other option is to use megahit for contig construction, then use a scaffolder such as SSPACE to exploit the paired-end reads to join contigs.

[shaman-narayanasamy]

@tseemann, will give both of these a try.

Thanks again for the tips!

[voutcn]

@shaman-narayanasamy We release a new version https://github.com/voutcn/megahit/releases/tag/v0.3.0-beta, in which PE informations are used by Megahit, please give it a try. We look forward to your feedbacks!

[tseemann]

Excellent news - will add support to our pipelines and see how it goes.

You can close this Issue now @shaman-narayanasamy

[shaman-narayanasamy]

@voutcn, great news! Haven't tested it yet. I will do it some time soon and provide you with some feedback as well. Closing issue.