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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Running nullarbor.pl on assembled genomes #243

Closed com31 closed 4 years ago

com31 commented 4 years ago

How can we run the nullarbor.pl with assembly option switched off? This may come handy when analysing already assembled genomes available in public databases.

tseemann commented 4 years ago

There is no way to do this in Nuillarbor, sorry. It is planned however.

We do have a --prefill option which we use here, to re-use existing assemblies. https://github.com/tseemann/nullarbor#prefilling-data You still need reads however.

The underlying Snippy tool has a special wrapper called snippy-multi which allows PE reads and Contigs in it's input file. But it only does the phylo tree and nothing else.

https://github.com/tseemann/snippy#using-snippy-multi

Other options may be to see if Bohra supports what you desire: https://github.com/kristyhoran/bohra