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Snakefile config
Francisco Zorrilla edited this page Mar 22, 2021
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14 revisions
The config.yaml
file contains a list of parameters that are read in by the Snakefile. Instead of editing the Snakefile whenever you want to try to change some parameter, just create a new copy of the config.yaml
file. Now thats what I call reproducibility.
- Quality filter reads with fastp
- Assembly with megahit
- Draft bin sets with CONCOCT, MaxBin2, and MetaBAT2
- Refine & reassemble bins with metaWRAP
- Taxonomic assignment with GTDB-tk
- Relative abundances with bwa
- Reconstruct & evaluate genome-scale metabolic models with CarveMe and memote
- Species metabolic coupling analysis with SMETANA