A Snakemake workflow for preparation of a curated catalogue of sequences of possible new tobamoviruses by scanning a large accumulated set of data from different metagenomics data repositories.
More info: http://projects.nib.si/tobamo/
The usage of this workflow is described in the Snakemake Workflow Catalog.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).
- Quality control and adapter trimming with Trimmomatic
- De Novo Assembly with megahit and SPAdes
- Search for similarity against all tobamoviral protein sequences with Diamond blastx
- Search for similarity against non-redundant (NR) protein database with Diamond blastx
- Assigning taxonomy with Megan6
