apclusterv 1.0.0

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Apclusterv: Clustering viral genomes with Affinity Propagation

This software works in Python3.

Dependencies:

python>=3.7
pandas
numpy
networkx >= 2.8.4
scipy >=1.8.1
scikit-learn >= 1.1.2
MCL
diamond >= 0.9.34
prodigal >= 2.6.3
R>=3.6.1

Installation:

Suppose you are in a conda environment, you need to install MCL, prodigal (for ORF prediction),diamond (for alignment) and R(if not already installed, we just need stats library in r-base)

conda install diamond -c bioconda 
conda install mcl -c bioconda
conda install prodigal -c bioconda
conda install r-base 

pip install apclusterv 

Getting Started:

step1. preduct ORFs from the DNA file with the following command:

prepare contig_dna_fasta 

(contig_dna_fasta is the path to the dna sequences for clustering)

step2. execute clustering with the following command:

apclusterv contig_dna_fasta 

Results

The program will create tmp/ directory. The clustering result is tmp/cluster_result.I.A.csv (cluster_result.3.10.csv by default)