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v0.2.1-SNPanalysisa3a2a86a · ·
Focus on SNP ANALYSIS This is the implemented workflow 1. call SNPs with snippy (also for samples with assemblies 'don't have reads') 2. (optionally) filter SNPs in phage regions 'BED file must be supplied in snippy-core -> params -> masked regions' TODO - Phage regions can be obtained by putting the reference genebank accession number in phaster -> tab seach by accession: https://phaster.ca/ 3. (optionally) filter SNPs in large_repitive_regions. True or False for auto-detection of repeats with nucmer 4. (optionally) filter for recombinant regions with gubbins 5. (optionally) filter for homoplasic SNPs with HomoplasyFinder 6. (optionally) exclude or include reference sequence in the final alignment before making phylogeny - useful in outbreaks analysed with distant reference 7. make a phylogeny - define phylogeny input (genome alignment with reference or without reference- recombination filtered or recombination and homoplasy filtered - define phylogeny algorithm and program: maximum liklihood tree (Fasttree, raxml or raxml-ng) or neighbor joining tree (Grapetree or Fastphylo) - midpoint rooting of the tree - phylogeny plot for publication 8. define clusters based on pairwise snp distances (hclust) & based on sequence alignment with fastbaps.
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