ddeemerpurdue / mag_contig_purifier

MAG_Contig_Purifier

Purpose:

To take an existing set of bins from a metagenomic analysis and repatriate non-binning contigs, remove contigs that contaminate bins, and eventually merge/split bins using a combination of de-novo and reference-based methods.

Outline

Starting point:

1. Raw assembly file(s)
2. Bin set
3. Bin identification file

• This is a tab-delimited file with two columns: bin_name and contig_name
• The bin_name should be in the format: "Bin.[number]"
• The contig_name should be in the format: ">[contig_name]"

Step 0: Standardize all inputs

Step 1a: Remove contamination from bins based on CATBAT annotation scores

Step 1b: Add contigs into bins based on CATBAT annotation scores

Step 2: Add contigs into bins based on ANI relations across samples

Step 3: Merge bins together based on multiple lines of evidence:

a. Shared taxonomy b. ANI patterns across samples c. Non-overlapping gene content