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Any alternative for SSPACE-longreads or any suggestion to speed up

Hi all,

I am using SSPACE-longreads to scaffold my genome (around 3G) with error corrected Pacbio data (10000000 reads), but the output is super slow, it seems the process will take 3 months. Is there any alternative to fulfill the same purpose? Or are there any suggestion to speed up, for example changing part of the code or any trick? BTW, I am using the default parameters.

genome assembly next-gen
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updated by Biostar Biostar • written by caizexi123 • caizexi123

Did you try using more CPU by changing the -T parameter?

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written by Sej Modha Sej Modha

Yes, 8 threads. But, the blasr just take couple hours to complete. And I think SSPACE-longreads don't run multi-thread after blasr.

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written by caizexi123 • caizexi123

what about PBJelly’s? Each step in PBJelly’s workflow can be run on a cluster

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written by Medhat Medhat

I am trying PBjelly now. Waiting for the result. But what else I can try?

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written by caizexi123 • caizexi123

AHA is part of SMRT Analysis, it seems too complicate to setup. I will try after the PBJelly finish.

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written by caizexi123 • caizexi123

1 answer

Maybe you can try OPERA-LG. It has a script for scaffolding using PacBio reads. Here is the paper https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0951-y

It seems to be better than SSPACE-LongReads

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written by felipe.zoujiro • felipe.zoujiro

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