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gbouras13 / hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
MIT License
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[Feature request] Add extra flags for running Flye #101

Closed pdobbler closed 1 month ago

pdobbler commented 1 month ago

Hi @gbouras13, thank you for hybracter!

Is your feature request related to a problem? Please describe.

I'm running 5 bacterial genomes through hybracter. These are high-depth sequencing done with nanopore. However, for 2 genomes, Flye fails with 'No disjointigs were found' error. It seems to be a problem when too much data is given to Flye.

I used the --subsample_depth 100 flag from hybracter without success.

Describe the solution you'd like Would it be too disruptive to add an option to add further options to run Flye? Something like: --extra-params-flye "--meta"

For these cases, it was suggested use --meta or subsampling during the disjointigs step

In this case, running Flye with --meta worked for my 2 genomes that were failing before.

Would a solution around this be possible?

gbouras13 commented 1 month ago

Hi @pdobbler

Very reasonable and easy request - luckily, I am planning on releasing a new version today implementing Medaka v2 and --bacteria after Ryan Wick's blogpost https://rrwick.github.io/2024/10/17/medaka-v2.html. So should be available soon.

George

gbouras13 commented 1 month ago

implemented in v0.10.0 - let me know if that works for you @pdobbler

pdobbler commented 1 month ago

That's great! Thank you @gbouras13, I'll give it a go now!