aviary

What problem does it solve?

Aviary automates the entire metagenomic analysis workflow, including assembly, binning, annotation, and dereplication, saving you time and effort in processing large-scale metagenomic data.

Core Features & Use Cases

• Assembly: Perform quality control and assembly of metagenomic reads, including short reads, long reads, and hybrid workflows.
• Binning: Extract MAGs from assemblies using multiple binning algorithms, including Rosella, MetaBAT2, SemiBin2, and VAMB.
• Annotation: Provide taxonomic and functional annotations for MAGs using GTDB-tk and EggNOG-mapper.
• Dereplication: Dereplicate MAGs across multiple runs using the cluster subcommand.
• Use Case: Imagine you have thousands of metagenomic samples. Use Aviary to automatically assemble, bin, annotate, and dereplicate all the samples, producing a comprehensive analysis of the metagenomic community.

Quick Start

Use the aviary skill to assemble and recover MAGs from the provided short and long reads.

aviary assemble -1 short_read_1.fq.gz -2 short_read_2.fq.gz -l long_read.fastq.gz -o output_dir/
aviary recover -a output_dir/assembly/final_contigs.fasta -o output_dir/