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SNP-based phylogenetic tree

Requirements

  • MUMmer v4.0.0beta2
  • FastTreeMP v2.1.10

You should be able to run the following from your command line:
nucmer
FastTreeMP

Locate viral genomes for an individual viral OTU and place these into a directory. Choose one of these genomes to be the representative
GENOMES=my_genomes
REP=my_genomes/representative.fna

Align all genomes to a selected representative
python align_genomes.py --genomes $GENOMES --ref $REP --out alignments

Use SNPs to build multiple sequence alignment
python build_msa.py --in alignments --out snps.fna --max_gaps_col 50 --max_gaps_seq 50

Use FastTree to contruct phylogeny
FastTreeMP snps.fna > snps.tree

Pipeline overview

  1. Use nucmer utility in MUMmer4 to align all genomes to a reference
  2. Call SNPs in 1:1 alignment blocks using show-snps, show-coords, and show-diff utlilties
  3. Use alignments to create multiple sequence alignments against reference
  4. Remove genomic sites covered in <50% of genomes and non-polymorphic sites (i.e. non-SNPs)
  5. Remove genomes containing >50% gaps
  6. Use FastTree to create phylogeny from trimmed multiple sequence alignment