This workflow automates the preprocessing of your genomic or metagenomic datasets.

To execute the workflow, run:

miga preproc_wf -o my_project -i raw_reads_single path/to/reads/*.fastq

Supported inputs include:

  • 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.