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Old 04-16-2016, 03:19 AM   #1
moistplus
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Location: Germany

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Default de novo assembly strategy for mid size genome and illumina reads ?

Hello,

I have illumina reads (PE and mate pair) and my expected genome size is about 500 M.

I plan to use use Soapdenovo. Do you have any other recommendation ?
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Old 04-18-2016, 08:39 AM   #2
westerman
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ABySS, Ray, Platanus. I have found that Soapdenovo produces supposedly good statistics via shoving contigs together. Not always the case.
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Old 04-18-2016, 05:15 PM   #3
skycreative
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Quote:
Originally Posted by westerman View Post
ABySS, Ray, Platanus. I have found that Soapdenovo produces supposedly good statistics via shoving contigs together. Not always the case.
Agree with you, as my experience, Soapdenovo lost some important regions during assebmly process
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Old 04-19-2016, 06:07 AM   #4
lac302
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SOAPdenovo2 or SGA for contig assembly..SSPACE for scaffolding
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