lorbin

name	lorbin
description	LorBin — unsupervised long-read metagenome binning with multiscale adaptive clustering (DBSCAN + BIRCH) and single-copy-gene evaluation. Use when: (1) Binning long-read / HiFi metagenome assemblies, (2) Recovering MAGs from species-rich or abundance-imbalanced communities, (3) Comparing LorBin to SemiBin2/VAMB long-read modes, (4) Feeding LorBin bins into ensemble refinement (BASALT `-e l` needs the PKU-EMBL LorBin fork). Upstream: https://github.com/LorMeBioAI/LorBin. For ensemble recovery use basalt. For short-read defaults use metabat2 / semibin2 / vamb.
license	MIT
category	analysis-tools
tags	["binning","long-read","LorBin","MAG","DBSCAN"]
upstream	https://github.com/LorMeBioAI/LorBin
stage	binning

LorBin

Upstream: LorMeBioAI/LorBin

Citation

Xue, W. et al. LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation. Nat. Commun. 16, 9353 (2025). https://doi.org/10.1038/s41467-025-64916-8

See also docs/references.md.

Analytical thinking

Long-read assemblies differ from short-read graphs: fewer, longer contigs, sharper abundance separation, and often unknown / imbalanced taxa. Short-read binners (and some DL tools trained mainly on short-read CAMI) under-recover novel lineages in that regime.

LorBin is an unsupervised long-read binner: multiscale adaptive DBSCAN then BIRCH, with iterative single-copy-gene evaluation to accept/recluster bins. The paper reports large gains in high-quality MAGs and novel taxa vs several competitors on oral, gut, and marine long-read sets — treat those as benchmark-conditioned, not universal guarantees.

Within this package:

Role	Skill
Long-read single binner	lorbin (or SemiBin2 long-read mode)
Short-read single binners	metabat2 · semibin2 · vamb · comebin
Ensemble refinement	basalt ★ · metawrap · dastool

If using BASALT with LorBin as an extra binner (-e l), use the PKU-EMBL LorBin fork commit documented in the BASALT guide — not an arbitrary upstream tip.

Prerequisites

Requirement	Notes
Assembly	Long-read / hybrid contigs (metaFlye, metaMDBG, …)
Coverage	BAM or abundance table as required by upstream CLI
QC	Always follow with checkm2 (+ gunc for chimera risk)

How to run

Verify flags against upstream README/--help (CLI evolves):

# illustrative — confirm exact subcommands in LorBin docs
lorbin \
  --contigs long_contigs.fa \
  --bam temp/map/*.bam \
  --outdir temp/bins/lorbin \
  --threads 32

Decision tree

Long-read MAG recovery?
├─ Dedicated long-read binner → lorbin
├─ SemiBin2 long-read / ensemble-DBSCAN path → semibin2
├─ Multi-binner + refinement (related samples) → basalt ★
└─ Only short reads → prefer metabat2 / semibin2 / vamb (+ ensemble)

Methods caveats

• Unsupervised clustering + SCG gates ≠ experimental species proof.
• Report assembler, read type (ONT/HiFi), LorBin version, and CheckM2 gates.
• Do not claim “novel phylum” from LorBin alone — require GTDB-Tk + literature placement and chimera screens (gunc).

Related skills

metaflye · metamdbg · semibin2 · vamb · basalt · checkm2 · gunc · tool-selection · metagenomics-workflow