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richarddurbin / hash10x

a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly
Apache License 2.0
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Question of de novo assembly #1

Open fangdm opened 4 years ago

fangdm commented 4 years ago

how to get the final assembly sequence? I guess we need moshmap or moshasm, could you give me an example? Thanks.

richarddurbin commented 4 years ago

I regret this code is incomplete, and there is nothing yet to provide a final assembly. Richard

On 20 Dec 2019, at 15:15, fangdm notifications@github.com wrote:

how to get the final assembly sequence? I guess we need moshmap or moshasm, could you give me an example? Thanks.

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fangdm commented 4 years ago

Well, assembly remains difficult with 10X Genomics linked read data. It is quite heavy to run with Supernova. Do you have a better way to finish it? Thank you.

richarddurbin commented 4 years ago

I am not impressed by Supernova, but just now I don’t know a better assembler for pure 10X data. Sorry.
We mostly use 10X for scaffolding, using Zemin Ning’s scaff10x, and also for phasing against a reference.

Richard

On 20 Dec 2019, at 16:23, fangdm notifications@github.com wrote:

Well, assembly remains difficult with 10X Genomics linked read data. It is quite heavy to run with Supernova. Do you have a better way to finish it? Thank you.

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