Introduction
Requirements
1. Get contigs that are/aren’t included in MAGs
1.1. Combine contigs files together for all sets of MAGs
1.2. Identify which contigs appear in final/nrMAGs
1.3. Taxonomic classification of contigs that aren’t in MAGs
Assuming that you’re already run the taxonomic assignment and understand this, so give abridged version?
2. Get best alignment for all reads
3. Collate read-by-read output for each sample
3.1. Collate all annotations for each read for each sample (if you didn’t already do this)
3.2. Get preferred annotation for each read for each sample
3.3. Combine this with MAG > contig > read-based
4. Collate output for all samples
Authors: Robyn Wright
First created: 16 October 2026
Last updated: 16 October 2026
Based on initial versions by: NA
