anvio

name	anvio
description	Anvi'o — interactive multi-omics platform for metagenomic assemblies, MAG refinement, visualization, and SNP/profile exploration. Use when: (1) Manual or human-guided bin refinement, (2) Interactive contig profiles across samples, (3) Linking MAGs with coverage/SNVs/metatranscriptomes, (4) Producing Anvi'o interactive HTML reports. Upstream: https://github.com/merenlab/anvio. Complements automated ensemble binning (basalt/metawrap/dastool); not a replacement for CheckM2/GUNC QC.
license	MIT
category	analysis-tools
tags	["anvio","visualization","MAG","refinement","interactive"]
upstream	https://github.com/merenlab/anvio
stage	binning

Anvi'o

Upstream: merenlab/anvio · https://anvio.org/

Citation

Eren, A. M. et al. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 3, e1319 (2015). https://doi.org/10.7717/peerj.1319

See also docs/references.md.

Analytical thinking

Anvi'o is a platform, not a single binner: contig databases, profiling BAM coverage across samples, interactive interfaces for organizing contigs into bins, SNV profiling, and multi-omics linking. Use it when automated bins need human-guided refinement or when you must communicate contig-level evidence.

Typical place in this package:

assembly + multi-sample BAMs
  → anvi'o contig DB + profile DB
  → import automatic bins (MetaBAT2 / BASALT / …) optional
  → interactive refinement
  → export bins → checkm2 / gunc / drep / gtdbtk

Do not treat interactive aesthetics as QC — still run checkm2 / gunc / deepurify as appropriate.

Prerequisites

Need	Notes
Contigs	Assembly FASTA
BAM(s)	Sorted/indexed; multi-sample profiles are Anvi'o's strength
RAM / GUI	Large profiles need memory; interactive needs browser access

How to run (pattern)

Exact subcommands evolve — verify with anvi-script-reformat-fasta --help / current docs:

# illustrative workflow skeleton
anvi-script-reformat-fasta contigs.fa -o contigs_fixed.fa --simplify-names
anvi-gen-contigs-database -f contigs_fixed.fa -o CONTIGS.db -n PROJECT
anvi-run-hmms -c CONTIGS.db -T 16
anvi-profile -i sample.bam -c CONTIGS.db -o PROFILE_sample -T 16
# anvi-merge ... then anvi-interactive -p PROFILE.db -c CONTIGS.db

Decision tree

Need interactive MAG refinement / multi-omics viz?
├─ Yes → anvio
├─ Fully automated catalogue → basalt ★ / metawrap / dastool
└─ Only QC metrics → checkm2 / gunc / mag-qc

Related skills

basalt · metawrap · coverm · checkm2 · gunc · deepurify · visualization · tool-selection mag-qc