BIOINFORMATICS WORFLOW
1
Introduction
1.1
Workflow overview
1.2
Snakemake pipeline
2
Data preprocessing
2.1
Quality-filtering
2.2
Splitting host and non-host data
Index host genome
Host mapping
2.3
Metagenomic complexity assessment
2.4
Prokaryotic fraction assessment
3
Assembly & Binning
3.1
Metagenomic assembly
3.2
Assembly mapping
3.3
Ensemble binning
3.3.1
Maxbin
3.3.2
Metabat
3.3.3
CONCOCT
3.4
Bin refinement
4
Bin annotation
4.1
Taxonomic annotation
4.2
Functional annotation
5
Dereplication and mapping
5.1
MAG dereplication
5.2
Mapping to MAG catalogue
References
Earth Hologenome Initiative
Laboratory workflow
Analysis workflow
The Earth Hologenome Initiative Bioinformatics Workflow
References