44![ OS] ( https://img.shields.io/badge/OS-Mac_|_Linux-steelblue )
55![ License] ( https://img.shields.io/badge/License-MIT-steelblue )
66[ ![ Latest PyPI version] ( https://img.shields.io/pypi/v/aniclustermap.svg )] ( https://pypi.python.org/pypi/aniclustermap )
7+ [ ![ Bioconda] ( https://img.shields.io/conda/vn/bioconda/aniclustermap.svg?color=green )] ( https://anaconda.org/bioconda/aniclustermap )
78
89## Overview
910
1011ANIclustermap is easy-to-use tool for drawing ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes.
1112
1213![ ANIclustermap.png] ( https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/small_dataset/ANIclustermap_annotation.png )
13- Fig1. ANIclustermap between all-vs-all 18 genomes. Areas where no similarity was found by fastANI are filled in gray.
14+ Fig1. ANIclustermap between all-vs-all 18 genomes. If no similarity detected by fastANI, filled in gray.
15+
1416![ ANIclustermap.png] ( https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/normal_dataset/ANIclustermap.png )
1517Fig2. ANIclustermap between all-vs-all 33 genomes.
1618
@@ -31,7 +33,8 @@ Install latest development version with pip:
3133Description of ANIclustermap's automated workflow.
3234
33351 . Calculate ANI between all-vs-all microbial genomes by fastANI.
34- If similarity between genomes is low, fastANI output NA. In that case, NA is replaced by 0.0.
36+ If no similarity detected by fastANI, NA is output. In that case, NA is replaced by 0.0.
37+ If previous result available at the time of re-run, reuse previous result.
35382 . Clustering ANI matrix by scipy's UPGMA method.
36393 . Using clustered matrix, draw ANI clustermap by seaborn.
3740
@@ -57,7 +60,7 @@ Description of ANIclustermap's automated workflow.
5760
5861### Example Command
5962
60- ANIclustermap -i ./example/input/minimal_dataset / -o ./aniclustermap_result
63+ ANIclustermap -i ./example/input/small_dataset / -o ./aniclustermap_result --fig_width 15
6164
6265## Output Contents
6366
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