Anvio

Anvi’o is a comprehensive platform that brings together many aspects of today’s cutting-edge computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-usefashion through extensive interactive visualization capabilities.

Anvio can be install using conda as follows and this is based on version 7.1 Reference:- https://anvio.org/

$ conda create -p /scratch/gencore/conda3/envs/anvio-7  python=3.6 -y
$ source  activate /scratch/gencore/conda3/envs/anvio-7
$ conda install -y -c bioconda "sqlite>=3.31.1"
$ conda install -y -c bioconda prodigal
$ conda install -y -c bioconda mcl
$ conda install -y -c bioconda muscle=3.8.1551
$ conda install -y -c bioconda hmmer
$ conda install -y -c bioconda diamond
$ conda install -y -c bioconda blast
$ conda install -y -c bioconda megahit
$ conda install -y -c bioconda spades
$ conda install -y -c bioconda bowtie2 tbb=2019.8
$ conda install -y -c bioconda bwa
$ conda install -y -c bioconda samtools=1.9
$ conda install -y -c bioconda centrifuge
$ conda install -y -c bioconda trimal
$ conda install -y -c bioconda iqtree
$ conda install -y -c bioconda trnascan-se
$ conda install -y -c bioconda r-base
$ conda install -y -c bioconda r-stringi
$ conda install -y -c bioconda r-tidyverse
$ conda install -y -c bioconda r-magrittr
$ conda install -y -c bioconda r-optparse
$ conda install -y -c bioconda bioconductor-qvalue
$ conda install -y -c bioconda fasttree
$ conda install -y -c bioconda vmatch
$ conda install -y -c bioconda fastani

Then download anvio package as follows:-

$ curl -L https://github.com/merenlab/anvio/releases/download/v7.1/anvio-7.1.tar.gz
$ pip install anvio-7.1.tar.gz