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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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variant calling and de novo assembly using sga #83

Closed SiyangLiu closed 8 years ago

SiyangLiu commented 10 years ago

Dear jared, Can SGA do de novo assembly and variant calling simultaneously? If so, how can I do that? Thank you very much in advance.

Best, Siyang

jts commented 10 years ago

Hi Siyang,

Yes it can but its not well documented yet. The first item on my todo list is officially releasing the variant calling module of SGA and providing examples. If you are feeling very adventurous you can have a look around this repository, which contains the driving code.

I'll update this issue when I've released the documentation.

Jared

SiyangLiu commented 10 years ago

Thank you very much. Have you ever evaluated the variant calling performance compared with the alignment-based variant calling tools? Do you have any impressions on the difference between a de novo assembly approach and the realignment approach? Perhaps the former is better for indel calling?

Best, Siyang

From: Jared Simpson Date: 2014-10-15 16:32 To: jts/sga CC: Siyang Subject: Re: [sga] variant calling and de novo assembly using sga (#83) Hi Siyang, Yes it can but its not well documented yet. The first item on my todo list is officially releasing the variant calling module of SGA and providing examples. If you are feeling very adventurous you can have a look around this repository, which contains the driving code. I'll update this issue when I've released the documentation. Jared — Reply to this email directly or view it on GitHub.

SiyangLiu commented 9 years ago

Dear Jared, Have you released the documentation yet? Thank you very much. Best, Siyang