Much larger assembly by soapdenovo2

[zhangd...@gmail.com]

Dear all,

I am trying to use SOAP2 to denovo assemble a bird species genome (~1.1Gb). I prepared 3 libraries, including 350 bp insertion PE libary (60Gb reads), 3kb MP library (30Gb reads) and 8kb MP library (30Gb reads), all are 150 bp PE sequenced.

I trimed adapters and remove PE contaminators for mate-pair libraries. PE library was adapter trimed and duplications removed. Then I tried soap2 using one step command,  but I always got a assembly of ~1.8 Gb, and this assembly was very very badly assembled (4 millions scaffolds).

How can I solve this problem?

Best regards,

Dezhi

[谢寅龙(Long Xie)]

Hi Dezhi,

You'd better do a kmer analysis and check if it's a highly duplicated or heterozygous genome. If so, you may try to get longer insertion data such as 20kb, or other platforms such as LFR or pacbio.

Best,

Yinlong Xie

MGI

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发件人: bgi-...@googlegroups.com <bgi-...@googlegroups.com> 代表 zhangd...@gmail.com <zhangd...@gmail.com>
发送时间: 2019年3月4日 11:45
收件人: BGI-SOAP
主题: [BGI-SOAP:1281] Much larger assembly by soapdenovo2

 

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