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README.md

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![OS](https://img.shields.io/badge/OS-Mac_|_Linux-steelblue)
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![License](https://img.shields.io/badge/License-MIT-steelblue)
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[![Latest PyPI version](https://img.shields.io/pypi/v/aniclustermap.svg)](https://pypi.python.org/pypi/aniclustermap)
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[![Bioconda](https://img.shields.io/conda/vn/bioconda/aniclustermap.svg?color=green)](https://anaconda.org/bioconda/aniclustermap)
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## Overview
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ANIclustermap is easy-to-use tool for drawing ANI(Average Nucleotide Identity) clustermap between all-vs-all microbial genomes.
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/small_dataset/ANIclustermap_annotation.png)
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Fig1. ANIclustermap between all-vs-all 18 genomes. Areas where no similarity was found by fastANI are filled in gray.
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Fig1. ANIclustermap between all-vs-all 18 genomes. If no similarity detected by fastANI, filled in gray.
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![ANIclustermap.png](https://raw.githubusercontent.com/moshi4/ANIclustermap/main/images/normal_dataset/ANIclustermap.png)
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Fig2. ANIclustermap between all-vs-all 33 genomes.
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Description of ANIclustermap's automated workflow.
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1. Calculate ANI between all-vs-all microbial genomes by fastANI.
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If similarity between genomes is low, fastANI output NA. In that case, NA is replaced by 0.0.
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If no similarity detected by fastANI, NA is output. In that case, NA is replaced by 0.0.
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If previous result available at the time of re-run, reuse previous result.
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2. Clustering ANI matrix by scipy's UPGMA method.
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3. Using clustered matrix, draw ANI clustermap by seaborn.
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### Example Command
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ANIclustermap -i ./example/input/minimal_dataset/ -o ./aniclustermap_result
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ANIclustermap -i ./example/input/small_dataset/ -o ./aniclustermap_result --fig_width 15
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## Output Contents
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