README.md

ANIclustermap

Overview

ANIclustermap is easy-to-use tool for drawing ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes. ANI between all-vs-all genomes are calculated by fastANI (or skani) and clustermap is drawn using seaborn.

Fig1. ANI clustermap between all-vs-all 33 genomes.

Fig2. ANI clustermap between all-vs-all 18 genomes. If no similarity detected by fastANI, filled in gray.

Installation

Python 3.8 or later is required for installation. fastANI or skani is required to calculate ANI.

Install bioconda package:

conda install -c conda-forge -c bioconda aniclustermap

Install PyPI stable package:

pip install aniclustermap

Workflow

Description of ANIclustermap's automated workflow.

1. Calculate ANI between all-vs-all microbial genomes by fastANI (or skani).
   If no similarity detected by fastANI, NA is output. In that case, NA is replaced by 0.0.
   If previous result available at the time of re-run, reuse previous result.
2. Clustering ANI matrix by scipy's UPGMA method.
3. Using clustered matrix, draw ANI clustermap by seaborn.

Usage

Basic Command

ANIclustermap -i [Genome fasta directory] -o [output directory]

Options

$ ANIclustermap --help
usage: ANIclustermap -i [Genome fasta directory] -o [output directory]

Draw ANI(Average Nucleotide Identity) clustermap

optional arguments:
  -i I, --indir I      Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta)
  -o O, --outdir O     Output directory
  -m , --mode          ANI calculation mode ('fastani'[default]|'skani')
  -t , --thread_num    Thread number parameter (Default: MaxThread - 1)
  --overwrite          Overwrite previous ANI calculation result (Default: OFF)
  --fig_width          Figure width (Default: 10)
  --fig_height         Figure height (Default: 10)
  --dendrogram_ratio   Dendrogram ratio to figsize (Default: 0.15)
  --cmap_colors        cmap interpolation colors parameter (Default: 'lime,yellow,red')
  --cmap_gamma         cmap gamma parameter (Default: 1.0)
  --cmap_ranges        Range values (e.g. 80,90,95,100) for discrete cmap (Default: None)
  --cbar_pos           Colorbar position (Default: (0.02, 0.8, 0.05, 0.18))
  --annotation         Show ANI value annotation (Default: OFF)
  --annotation_fmt     Annotation value format (Default: '.3g')
  -v, --version        Print version information
  -h, --help           Show this help message and exit

Example Command

7 genomes minimal dataset. Click here to download dataset (Size=3.6MB).

ANIclustermap -i ./minimal_dataset/ -o ./ANIclustermap_result

Output Contents

ANIclustermap outputs 3 types of files.

• ANIclustermap.[png|svg] (example1, example2)
  ANI clustermap result figure.

• ANIclustermap_matrix.tsv (example)
  Clustered all-vs-all ANI matrix.

• ANIclustermap_dendrogram.nwk (example)
  Newick format clustering dendrogram.

Gallery

Example gallery of 33 genomes normal dataset.
If you want to try it for yourself, click here to donwload dataset (Size=63.5MB).

Normal parameter:

ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \
              --fig_width 15

Change cmap_gamma parameter:

ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
              --fig_width 15 --cmap_gamma 0.5

Change cmap_colors(=white,orange,red) paramter:

ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
              --fig_width 15 --cmap_colors white,orange,red

Change cmap_ranges paramter:

ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
              --fig_width 15 --cmap_ranges 80,85,90,92.5,95,97.5,100

See this issue for more details.

Add ANI value annotation parameter:

ANIclustermap -i ./normal_dataset -o ./ANIclustermap_result \ 
              --fig_width 20 --fig_height 15 --annotation