MagentaFlow - quadram-institute-bioscience/gmh-sops GitHub Wiki
MagentaFlow
Metagenomics and Metaviromics pipeline
MagentaFlow is a workflow for the analysis of whole metagenome shotgun experiments (using Illumina Paired-End libraries).
It consists of:
- QC (fastp 0.20.1)
- Read-by-read analysis
- De novo assembly (MEGAHIT v1.2.9)
- Gene prediction (Metaprokka 1.14.6c)
- Binning (using both MaxBin 2.2.7 and MetaBat 2.15, refining and combining the two using DAS_Tool 1.1.2)
- Functional analysis (eggNOG mapper 2.0.1)
- Backmapping (bbmap 38.57)
- Under costruction