Taxonomy placement of viral OTUs
vConTACT2 is a tool to infer the taxonomic relationship of viral sequences with a network-based approach, based on whole genome gene-sharing profiles.
To make use of its output there is a tool called graphanalyzer, and its repository comes with a tutorial.
The programme
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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
