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tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
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How to construct a recombination free core SNP phylogenetic tree using snippy and gubbins? #488

Open Jessie940409 opened 3 years ago

Jessie940409 commented 3 years ago

Hi， I'm new to this and I want to construct a recombination free core SNP phylogenetic tree using snippy and gubbins. I'm confused because core.aln is a core SNP alignment file and core.full.aln is a whole genome SNP alignment file, while the input of gubbins should be a whole genome alignment file. So what should I do to get a recombination free core SNP phylogenetic tree?? Can I use core.aln as the input of gubbins?

After I got core.full.aln, if I run this: %snippy-clean_full_aln core.full.aln > clean.full.aln %run_gubbins.py -p gubbins clean.full.aln %snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln %FastTree -gtr -nt clean.core.aln > clean.core.tree

In this case, this clean.core.tree is a recombination free core SNP phylogetneic tree or a recombination free whole SNP phylogetneic tree ???

Best wishes Jessie

liuxq000 commented 1 year ago

Hello, I have the same problem, I don't know if the end result is a core SNP phylogetneic tree. Can you help me？