Long reads support about hecatomb HOT 5 OPEN

Hi, sorry it might not be that obvious. Run Hecatomb like so:
hecatomb run --trim filtlong ...
I would probably also use --assembly cross if you dont have too many samples, but for hifi reads you might want to try an assembler and parameters better tuned for hifi reads.

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Thanks for the reply. Can I apply contigs to conduct partial hecatmob pipeline?

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Sure! If you just want the read-annotations without the assembly, just add 'read_annotations' to specify the target output files:
hecatomb run read_annotations ...

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Thanks for the reply! Just complete the read_annotations option, but can I apply assembled contigs into hecatomb process?

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Not easily. It would probably be easier to manually run mmseqs searches of the contigs against the secondary databases.

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