Gathering the (virome) tools
A short overview of tools used and how to get them
Install “conda” (and “mamba”)
Conda is pre-installed in EBAME VMs. Check the EBAME-7 notes for more details.
Miniconda is a package manager widely adopted in bioinformatics, as it allows to install and manage software packages with minimal effort and also to create isolated environments for each project, which can be exported and shared with others.
Mamba is a drop-in replacement for the conda package manager,
which is faster and more efficient than conda. In simple terms, replacing
conda with mamba will speed up the installations, as long as Mamba
itself was installed with conda install -c conda-forge mamba.
- Read more about how to rinstall Miniconda and Mamba
What tools
- A de novo assembly program, such as MegaHit or Spades. They are both readily available from BioConda
- One or more viral mining tools, such as VirSorter2 (BioConda)
- A classifier: Phanta
Some programs are fully available as BioConda packages, and simply
1
mamba install -c conda-forge -c bioconda megahit
will install the assembler.
Viromic programs sometimes are either unavailable from BioConda or they require further steps to download the databases.
The programme
-
EBAME-22 notes: EBAME-7 specific notes -
Gathering the reads:
downloading and subsampling reads from public repositories (optional) -
Gathering the tools:
we will use Miniconda to manage our dependencies -
Reads by reads profiling:
using Phanta to quickly profile the bacterial and viral components of a microbial community -
De novo mining:
assembly based approach, using VirSorter as an example miner -
Viral taxonomy:
ab initio taxonomy profiling using vConTACT2 -
MetaPhage overview:
what is MetaPhage, a reads to report pipeline for viral metagenomics
