raw_reads_single: Single raw reads in a single FastQ file
raw_reads_paired: Paired raw reads in two FastQ files
trimmed_reads_single: Single trimmed reads in a single FastA file
trimmed_reads_paired: Paired trimmed reads in two FastA files
trimmed_reads_interleaved: Paired trimmed reads in a single FastA file
assembly: Assembled contigs or scaffolds in FastA format
For additional options, run:
miga preproc_wf -h
Expected output
Once your run is complete, you may expect the standard summaries for cds, assembly, essential_genes, and ssu. Additionally all the intermediate files are preserved, including assemblies, predicted genes, and detected essential and ribosomal genes.