metaflye

name	metaflye
description	Long-read metagenome assembly with Flye/metaFlye. Use this skill when working with metaflye: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/fenderglass/Flye. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["assembly","long-read"]
upstream	https://github.com/fenderglass/Flye
stage	assembly

metaFlye

Upstream: metaFlye

Citation

Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020). https://doi.org/10.1038/s41592-020-00971-x

See also docs/references.md.

Analytical thinking

Primary long-read metagenome assembler for noisy ONT/PacBio CLR. For HiFi prefer metaMDBG/hifiasm-meta. Still map reads back for binning.

How to run

conda install -c bioconda flye  # if packaged; else follow upstream

flye --meta --nano-raw reads.fastq.gz --out-dir temp/asm/flye -t 32
# or --pacbio-raw / --nano-hq per chemistry

Key parameters

| --meta | metagenome mode | Required | | read type flag | match chemistry | |

Decision notes

• Stage: assembly (long-read metagenomes)
• Prefer ONT/PacBio community assemblies; polish when chemistry requires
• Downstream: long-read-aware binning (lorbin, SemiBin2 LR)

Related skills

minimap2 · metamdbg · megahit · metaspades · tool-selection · metagenomics-workflow