Metapathways can be run as an atomic step, but it is really a pipeline composed of multiple other steps. Full value lies in porting the steps in the Metapthways pipelines to maximize modularity.
Core functional annotation pipeline exists in the form of prodigal -> alignment-based search (BLAST, FAST, Diamond)
Remaining features needed for Metapathways replacement
- read coverage module (contigs + reads -> depth per contig)
- identify rRNA and align to silva
- tRNA scan
- genbank output
There is also integration with pathologic, but pathologic is not easily obtainable or usable so it will be left out of scope for this request.
Metapathways can be run as an atomic step, but it is really a pipeline composed of multiple other steps. Full value lies in porting the steps in the Metapthways pipelines to maximize modularity.
Core functional annotation pipeline exists in the form of prodigal -> alignment-based search (BLAST, FAST, Diamond)
Remaining features needed for Metapathways replacement
There is also integration with pathologic, but pathologic is not easily obtainable or usable so it will be left out of scope for this request.