Output.md

Output files

All output files are stored in a folder with the same name as the sampleID in the specified output directory. If no output directory is specified, the files are stored in the current working directory.

Folder structure

sampleID/
├── qc/
│   ├── shortread_qc/       (hybrid only)
│   ├── longread_raw/
│   ├── longread_filterd/
│   ├── assembly_qc/
│   └── qc_sampleID.json
├── assembly/
│   ├── graph_plot/         
│   ├── miniasm/            (if mode selected)
│   ├── spades/             (if mode selected)
│   ├── unicycler/          (if mode selected)
│   ├── canu/               (if mode selected)
│   └── flye/               (if mode selected)
├── assembly_processed/
│   ├── racon/              (if mode selected)
│   ├── pilon/              (if mode selected)
│   └── link/               (if mode selected)
├── plasmid_analysis/
├── genomes/    
└── plasmids/