metawrap

name	metawrap
description	MetaWRAP suite for multi-binner MAG recovery and CheckM-style bin refinement — one option in the ensemble binning family (with DAS Tool and BASALT). Use this skill when working with metawrap: installing, choosing parameters, running binning/bin_refinement/reassemble_bins, or troubleshooting. Upstream: https://github.com/bxlab/metaWRAP. Prefer basalt as the recommended ensemble default for related multi-assembly work; use dastool for classical contig2bin aggregation. For routing, use tool-selection.
license	MIT
category	analysis-tools
tags	["MAG","ensemble-binning","binning","metabat","maxbin"]
upstream	https://github.com/bxlab/metaWRAP

MetaWRAP

Upstream: bxlab/metaWRAP

Citation

Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018). https://doi.org/10.1186/s40168-018-0541-1

See also docs/references.md.

Analytical thinking

MetaWRAP is a module suite in the ensemble binning family (alongside DAS Tool and BASALT). For MAG recovery the critical path is binning → bin_refinement (± reassemble_bins). Refinement consolidates MetaBAT2/MaxBin2/(CONCOCT) predictions; refinement thresholds (-c/-x) are scientific choices, not mere software defaults.

Recommended default in this package: basalt (especially related samples / multi-assembly refinement). Choose MetaWRAP when you want a classical packaged multi-binner + refinement catalogue on a single assembly workflow. Choose dastool when you already have contig2bin tables and only need SCG aggregation.

Depth guidance: ~≥6 Gb/sample typical; complex soils often ≥30 Gb.

How to run

metawrap binning -o temp/bin -t 32 \
  -a contigs.fa --metabat2 --maxbin2 \
  reads/*_1.fastq reads/*_2.fastq
# CONCOCT optional; costly

metawrap bin_refinement -o temp/bin_refine -t 32 \
  -A temp/bin/metabat2_bins/ \
  -B temp/bin/maxbin2_bins/ \
  -c 50 -x 10

Modes: mixed co-assembly, per-sample, or subgroup binning for huge cohorts.

Key parameters

Module flag	Typical	Thinking
--metabat2 --maxbin2	on	Core pair; add CONCOCT if affordable
bin_refinement -c/-x	50 / 10	Publication-oriented; stricter → fewer bins
reassemble_bins	optional	Per-bin reassembly; validate with CheckM2

Decision tree

Ensemble MAG recovery?
├─ Recommended (related / multi-assembly) → basalt
├─ Packaged multi-binner + CheckM refinement suite → metawrap
└─ Classical SCG aggregation of contig2bin sets → dastool

Literature notes (Microbiome 2018)

Uritskiy et al. position MetaWRAP as a modular suite (raw reads → bins → bin analysis) with hybrid consolidation that outperformed individual binners and other consolidation tools on synthetic and real data in that paper.

Operational takeaways for this package:

• Critical MAG path: binning → bin_refinement (± reassemble_bins).
• Refinement -c/-x (completeness/contamination) are scientific thresholds — report them; they are not universal truth.
• Modules are standalone — you may use refinement on bins from outside MetaWRAP.
• Reassembly can improve bins but costs CPU/IO; reserve for priority genomes.
• For related multi-assembly refinement beyond classical MetaBAT/MaxBin suites, prefer basalt; keep MetaWRAP when you want the packaged CheckM-era refinement catalogue.

Related skills

basalt · dastool · megahit · drep · coverm · gtdbtk · checkm2 · mag-qc