Results Overview

The primary outputs are produced by bin/maggic_results.py, which aggregates quality metrics, taxonomic classification, mobile genetic element detection, and AMR profiling from all binning tools into structured results.

MultiQC HTML Report

MAGGIC generates an interactive MultiQC HTML report consolidating all pipeline outputs into a single browsable file.

The Data Summary cards provide a quick overview:

• Bin Classification: Total bins detected, breakdown by bin type (Chromosome, Plasmid, Mixed, Virus MAGs)
• Bacterial Confidence: High/Medium/Low confidence bins based on CheckM2 quality thresholds
• Antimicrobial Resistance: Total AMR genes detected and unique AMR classes
• Top 10 Taxa: Most abundant genera across all bins

The report includes the following sections:

• Chromosome Table: Sortable Chromosome_MAG rows (see Bin-Classification)
• Plasmid Table: Sortable Plasmid_MAG and Mixed_MAG rows (see Plasmid-Virus-Metrics)
• Virus Table: Sortable Virus_MAG rows (see Plasmid-Virus-Metrics)
• Sequence Quality Reports: Read quality from fastp or filtlong
• MAGGIC Plots: Diagnostic plots from maggic-wand (see MAGGIC-Plots)

Output Files (maggic_results folder)

File	Description
maggic-results.tsv	Full 30-column results table (all bins, all columns)
maggic-results-chromosome.tsv	Chromosome_MAG bins only (15 columns)
maggic-results-plasmid.tsv	Plasmid_MAG and Mixed_MAG bins (21 columns)
maggic-results-virus.tsv	Virus_MAG bins only (14 columns)
maggic-globalabundance.tsv	Merged CoverM coverage matrix (rows=bins, columns=samples)

Each table excludes irrelevant columns so you see only fields appropriate for that bin type.

Column Reference

Column	Source	Calculation
Name	MAGGIC bin name	Bin identifier from Binette quality report
Bacterial_Confidence	MAGGIC	Assigned based on quality and taxonomy thresholds (see Bin-Classification)
Taxonomy	GTDB-Tk classify_wf	Full GTDB taxonomy string from release232 classification
Completeness	Binette quality report	CheckM2 completion percentage
Contamination	Binette quality report	CheckM2 contamination percentage
Closest_Ref_ANI	GTDB-Tk	Average nucleotide identity to closest reference genome
Closest_Ref_AF	GTDB-Tk	Alignment fraction to closest reference genome
Genome_Size	Binette quality report	Total bin length in base pairs
Total_Contigs	Binette quality report	Number of contigs in the bin
GC_Content	Not implemented yet in MAGGIC	NA (placeholder value)
N50	Binette quality report	Contig N50
Coding_Density	Binette quality report	Fraction of bin annotated as coding
Plasmid_Fraction	Binette quality report + geNomad plasmid_summary.tsv	Fraction of total contigs with plasmid_score >= 0.75 (uses Binette contig_count as denominator, not plasmid_summary.tsv row count)
Plasmid_Length_Weighted_Score	geNomad plasmid_summary.tsv	Length-weighted mean plasmid_score: sum(score_i * length_i) / sum(length_i). Falls back to simple mean if lengths unavailable. PlasMAAG approach (Lindez et al. 2026). In plasmid TSV output, column is renamed to Length_Weighted_Score
Virus_Length_Weighted_Score	geNomad virus_summary.tsv	Length-weighted mean virus_score: sum(score_i * length_i) / sum(length_i). Falls back to simple mean if lengths unavailable. In virus TSV output, column is renamed to Length_Weighted_Score
Plasmid_Signal_Uniformity	geNomad plasmid_summary.tsv	How uniform the plasmid signal is across contigs. High if length-weighted score >= 0.9 AND min score >= 0.8; Medium if length-weighted score >= 0.7 AND min score >= 0.5; Low otherwise (see Plasmid-Virus-Metrics)
Virus_Count	geNomad virus_summary.tsv	Number of viral/viral-like contigs (phages, proviruses, other MGEs)
High_Conf_Viruses	geNomad virus_summary.tsv	Contigs with virus_score >= 0.9 AND FDR <= 10%
Virus_Signal_Uniformity	geNomad virus_summary.tsv	How uniform the viral signal is across contigs. High if length-weighted score >= 0.9 AND min score >= 0.8 AND no proviruses; Medium if proviruses present with high scores, or length-weighted score >= 0.7 AND min score >= 0.5; Low otherwise. Proviruses (integrated prophages) reduce confidence from High to Medium (Camargo et al. 2024)
Provirus_Count	geNomad virus_summary.tsv	Contigs with topology == Provirus; potentially physically integrated into the bin
Provirus_Fraction	geNomad virus_summary.tsv	provirus_count / virus_count
Mobility_Potential	MAGGIC	Pipe-separated evidence summary: plasmid:High|virus:Low|proviruses:2|mob:Relaxed,Mobilized where mob types come from geNomad plasmid_summary.tsv. Components appended only if present; none if no MGE evidence
Virus_Taxonomy	geNomad virus_summary.tsv	Semicolon-separated unique virus taxonomy strings
Plasmid_Count	geNomad plasmid_summary.tsv	Number of plasmid contigs
High_Conf_Plasmids	geNomad plasmid_summary.tsv	Contigs with plasmid_score >= 0.9 AND FDR <= 10%
Conjugation_Genes	geNomad plasmid_summary.tsv	Semicolon-separated mobilization gene types
AMR_Gene_Count	AMRFinderPlus	Number of hits with Type == "AMR" or Type == "STRESS" (excludes DISINFECTANT, HEAVY_METAL)
AMR_Classes	AMRFinderPlus	Semicolon-separated unique AMR classes
AMR_Genes	AMRFinderPlus	Semicolon-separated unique gene symbols