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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Disable maxseqlength and minseqlength by default #459

Closed mirajaonison closed 2 years ago

mirajaonison commented 3 years ago

I ran into a big issue because the --maxseqlength filtered out contigs from my genome assembly that were longer than 50,000 bp.

I would be better to remove the limit if the option is not set.

Regards

torognes commented 2 years ago

The reason for the setting is that vsearch becomes relatively slow with long sequences. It is designed for much shorter sequences. It should issue a warning when sequences are excluded.

torognes commented 2 years ago

I think we will leave it as it is. I will close the issue.