| 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.
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| 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
flye --meta --nano-raw reads.fastq.gz --out-dir temp/asm/flye -t 32
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
