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rhysnewellrhysnewellCommunity·1 Agent Skills Included

aviary

Metagenome assembly, genome binning, and annotation pipeline

Assembles metagenomic short, long, and hybrid sequencing reads into contigs, then recovers metagenome-assembled genomes using multiple binning algorithms. Annotates recovered genomes with taxonomic and functional databases, and dereplicates results across many runs. Removes the need to manually chain dozens of bioinformatics tools, with automatic database downloads and resumable workflows.
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npx skills add rhysnewell/aviary --all -g -y

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aviary

Automate metagenomic assembly, binning, annotation, and dereplication workflows.

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Frequently Asked Questions

FAQPage Schema
How to install Aviary?▼

Run `npx skills add rhysnewell/aviary --all -g -y` in your terminal to install all skills in this suite globally.

What does Aviary do?▼

Aviary runs a complete metagenomics workflow: read quality control, de novo assembly, genome binning with multiple algorithms, and taxonomic plus functional annotation of recovered genomes.

Does Aviary support long-read sequencing data?▼

Yes. It handles short reads, long reads (Nanopore and PacBio), and hybrid assemblies combining both, with assemblers like metaSPAdes, MEGAHIT, Flye, and myloasm.

What databases does Aviary need?▼

It requires GTDB, EggNOG, CheckM2, and SingleM databases, which can be downloaded automatically using the configure command with the download flag.

Can Aviary combine results from multiple samples?▼

Yes. The cluster command combines and dereplicates genomes from many separate Aviary runs into a single non-redundant set using Galah.

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