ANIm analysis

1 Analysis

The Average Nucleotide Identity (ANIm) analysis can be found in the assets/analysis/2021-06-19_ANIm repository subdirectory.

ANIm was conducted using pyani v0.3.0 with the commands:

pyani createdb -v -l pyani_logs/00-createdb.log
pyani index -v -l 01-index.log \
  bolteae_clostridioforme_symbiosum_genomes \
  --labels labels.txt \
  --classes classes.txt
pyani anim --debug -l 02-anim.log \
  -i bolteae_clostridioforme_symbiosum_genomes \
  -o anim_out \
  --scheduler SLURM \
  --labels bolteae_clostridioforme_symbiosum_genomes/labels.txt \
  --classes bolteae_clostridioforme_symbiosum_genomes/classes.txt
pyani plot -v -l 03-plot.log \
  anim_plots 1 \
  --formats png,pdf

# hybrid assembly genomes added; labels/classes files updated manually
# in new_labels.txt, new_classes.txt

pyani anim --debug -l 04-anim_hybrid.log \
  -i bolteae_clostridioforme_symbiosum_genomes \
  -o anim_out_hybrid \
  --scheduler SLURM \
  --labels bolteae_clostridioforme_symbiosum_genomes/new_labels.txt \
  --classes bolteae_clostridioforme_symbiosum_genomes/new_classes.txt
pyani plot -v -l 03-plot.log \
  anim_plots_hybrid 3 \
  --formats png,pdf

2 Output

The analysis files, including input genomes, are in the repository subdirectory assets/analysis/2021-06-19_ANIm.

The pyani database is in the file 2021-06-19_ANIm/pyanidb/pyanidb. Graphical output is in the directories 2021-06-19_ANIm/anim_plots and 2021-06-19_ANIm/anim_plots_hybrid. Log files cataloguing the analysis are in the 2021-06-19_ANIm/*.log files.