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gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
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Provide core gene alignments #85

Closed oschwengers closed 3 years ago

oschwengers commented 4 years ago

Hi, thanks a lot for this wonderful potential replacement for Roary which is not actively maintained anymore.

Would it be possible to create a core genome alignment just like Roary does (core_gene_alignment.aln) for subsequent tree calculations? Or is it already implemented and I just missed it?

Best regards!

nzmacalasdair commented 4 years ago

Hello! You should be able to create core genome alignments, like roary, with the -a core option when running panaroo. It's also possible to specify the aligner used as well.

If you've already run the pangenome inference step of panaroo and would like to create a core or pan genome alignment from that run, you can use panaroo-msa (or panaroo-msa-runner.py if you have installed panaroo by cloning the github) to create alignments from a completed run.

Hope this helps, let us know if you run into any further issues!

oschwengers commented 3 years ago

Hello, and thanks for the hint. One prank process exited != 0 and thus, there was no core alignment. I've tried it via panaroo-msa --aligner mafft which worked as expected.