Computational Biology Lab Wiki

Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.

It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs.

Anvi'o is installed using a virtualenv and it has several dependencies. First of all activate the virtualenv.

An example of an script:

## Anvio script

#!/bin/bash

### #activate virtualenv ####

source /home/soft/anvio/bin/activate

## Samtools

export PATH=/home/soft/samtools-1.3.1/:$PATH

## Prodigal

export PATH=/home/soft/Prodigal-2.6.2/:$PATH

## Hmmer

export PATH=/home/soft/hmmer-3.1b2/src:$PATH

## HDF5

export PATH=/home/soft/qiime/dependencies/hdf5-1.10.1/bin:$PATH

## GNU SciLib

export PATH=/home/soft/gsl-2.4/gsl:$PATH

export LD_LIBRARY_PATH=/home/soft/gsl-2.4/lib:$LD_LIBRARY_PATH

export PATH=/home/soft/gsl-2.4/lib:$PATH

# and this is an example

cd ~/ANVIO # you work directory

anvi-init-bam 04_MAPPING/B-RAW.bam -o 04_MAPPING/B.bam # anvio has different programs, this is just one of them for a specific step

### closing virtualenv ###

deactivate