MetaPhage, automated reads-to-report pipeline
MetaPhage is a complete reads-to-report pipeline for viral metagenomics. It is a Nextflow pipeline that can be run on a local machine or on a cluster. It is designed to be easy to use and to provide a complete report of the analysis.
See:
- a quick overview
- MetaPhage paper (Open Access)
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
