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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: