searching against PLSDB as an additional option in plassembler

gbouras13 / plassembler

Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

MIT License

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Closed gaworj closed 8 months ago

gaworj commented 9 months ago

Hi,

Thanks again for such a great tool! It is great to see new plassembler options.

Can you also add an option to search for user-supplied plasmids against PLDSB?

Bests, Jan

gbouras13 commented 9 months ago

Hi @gaworj ,

Thanks mate - let me know if you have any feedback on the long mode especially.

Do you mean to use mash to query input assemblies against the PLSDB? Like plassembler assembled with no copy number estimation?

Maybe I can just add a --no_copy_numbers flag to plassembler assembled that should hopefully do what you want.

George

gbouras13 commented 8 months ago

Hi @gaworj,

I've implemented this with --no_copy_numbers in the subcommand plassembler assembled

George