Kraken2 is run to generate output reports and separate classified contigs from unclassified.
A custom script separates each classified group of contigs into separate files at a specified taxonomic level (default level: genus). Output files are labeled as [Sample Name]_[Genus] to allow for easy post processing.
Input
Contig file (fasta) from the FinalAssembly dir
This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)