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gbouras13 / dnaapler

Reorients assembled microbial sequences
MIT License
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min and max length criteria #71

Open sejmodha opened 10 months ago

sejmodha commented 10 months ago

Hi There,

Thanks for developing this cool tool! It is indeed very useful for polishing assemblies.

I recently came across an issue whereby dnaapler was failing when a custom sequence specified for reorientation did not exist in one of the contigs in a multi-FASTA file. Ideally, an option to exclude/include length criteria could easily fix such an error by excluding such short/long contigs from the reorientation step and adding them onto the final results as it is.

Additionally, I noted that the bulk option can only be used for a multi-FASTA and fails when the input is a single sequence FASTA file. This causes a bit of an issue when such a tool is integrated into a workflow or a pipeline as typically the output or number of contigs generated using a de novo assembly step is unknown.

Thanks once again for developing dnaapler. Sej

gbouras13 commented 10 months ago

Hi @sejmodha ,

Thanks for the kind words mate.

With the first option, I will have a look into it - do you have an example input to share? I have not come across this bug before.

With the second option - I can relax this if you think it would be useful.

George