aniclustermap 0.1.0

A tool for drawing ANI clustermap between all-vs-all microbial genomes

ANIclustermap: Draw Clustermap of All-vs-All ANI

Overview

ANIclustermap is easy-to-use tool for drawing ANI clustermap between all-vs-all microbial genomes.

Installation

ANIclustermap is implemented in Python3. fastANI is required to calculate ANI.

Install PyPI stable version with pip:

pip install aniclustermap

Install latest development version with pip:

pip install git+https://github.com/moshi4/ANIclustermap.git

Workflow

Description of ANIclustermap's automated workflow.

1. Calculate ANI between all-vs-all microbial genomes by fastANI.
   If similarity between genomes is low, fastANI output NA. In that case, NA is replaced by 0.0.
2. Clustering ANI matrix by scipy's UPGMA method.
3. Using clustered matrix, drawing clustermap by seaborn.

Usage

Basic Command

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

Options

-h, --help           show this help message and exit
-i I, --indir I      Input genome fasta directory (*.fa|*.fna[.gz]|*.fasta)
-o O, --outdir O     Output directory
-t , --thread_num    fastANI thread number parameter (Default: 11)
--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)
--annotation         Show ANI value annotation (Default: OFF)
-v, --version        Print version information

Example Command

ANIclustermap -i ./example/minimal_dataset/ -o ./aniclustermap_result

Output Contents

ANIclustermap outputs 3 types of files.

• ANIclustermap.[png|svg]
  ANI clustermap result figure.

• ANIclustermap_matrix.tsv
  Clustered all-vs-all ANI matrix.

• ANIclustermap_dendrogram.nwk
  Newick format clustering dendrogram.