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fmalmeida / MpGAP

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
https://mpgap.readthedocs.io/en/latest/
GNU General Public License v3.0
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Add hifiasm for long reads assemble #53

Closed scintilla9 closed 4 months ago

scintilla9 commented 8 months ago

Hi Dr Almeida,

Thank you for the detailed genome assembly workflow. Could you please include another assembler, hifiasm(https://github.com/chhylp123/hifiasm)? It is particularly suited for long-read data

Best Chia-Wei

fmalmeida commented 8 months ago

@scintilla9 , Sure thing. I think it has been on my plate for some time. I you work on including it for v3.2 which is currently being tested in dev branch.

scintilla9 commented 4 months ago

Hi @fmalmeida

I would like to work on it recently. And I noticed that when building environment on my local machine with Dockerfile in dev, the building process will fail due to the url for downloading busco database is no available.

fmalmeida commented 4 months ago

Hi @scintilla9 , Thanks for wanting to help with this. And yes, the resources of it were deleted. I faced the same when trying to work on another issue (#50). Basically, I have it fixed but not merged to dev yet as I did not finish its implementation yet ( I am changing to do the BUSCO run manually instead of by Quast).

So, for you to start working on this one, I would recommend creating a branch from the branch: 50-add-skip-parameter-for-sreads-polishers-and-fix-multiqc-report-names

Are you working on your own fork? If so, would need to "sync" the fork with mine, to have this branch in your repo so that you can create a branch from it.

Otherwise, I can create the branch for you in this repo.

scintilla9 commented 4 months ago

Thanks for the information. I have created my own fork, and will let you know if I got any questions.

fmalmeida commented 4 months ago

Hi @scintilla9 , I merged the code to the dev branch. As said in the PR, I will start the full dataset testings to guarantee I can make a new release. Also, I opened a follow-up ticket now that hifiasm is available: #71 Many thanks for the contribution.