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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Gubbins using the WGS alignment created using contigs #358

Closed snackens closed 1 year ago

snackens commented 1 year ago

Hi, thank you for this great tools.

I'd like to detect recombination regions using gubbins. I'm going to use Snippy to create whole genome sequence alignment file for gubbins.

% snippy-clean_full_aln core.full.aln > clean.full.aln % run_gubbins.py -p gubbins clean.full.aln

One concern is that my dataset includes both complete geneome and contig level genome(90 % of my dataset are contig level). Finally I'd like to construct phylogenetic tree. In this case, are there any problems regarding using a lot of contig level genomes?

Best regards,

nickjcroucher commented 1 year ago

I would exclude poor quality draft assemblies that are likely to be contaminated/generated from low coverage data, but otherwise we have not encountered problems with this approach (e.g. here).