Automate metagenomic assembly, binning, annotation, and dereplication workflows.
npx skills add https://github.com/rhysnewell/aviary --skill aviary
Please help me install this Agent Skill. Skill: aviary Source: https://github.com/rhysnewell/aviary/tree/main/docs Command: npx skills add https://github.com/rhysnewell/aviary --skill aviary
Aviary automates the entire metagenomic analysis workflow, including assembly, binning, annotation, and dereplication, saving you time and effort in processing large-scale metagenomic data.
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/
High-intent search queries and answers about installing and using this skill.
Automate metagenomic assembly, binning, and annotation by running an integrated workflow that supports short reads, long reads, and hybrid inputs. It processes thousands of metagenomic samples end-to-end, recovering, annotating, and dereplicating MAGs automatically.
Taxonomic annotation and quality control of recovered MAGs require GTDB-tk, EggNOG-mapper, CheckM2, SingleM, and Metabuli. These dependencies provide functional annotations and assess genome completeness throughout the metagenomic workflow.
Dereplicate metagenome-assembled genomes across multiple runs using the cluster subcommand. This consolidates redundant MAGs from separate analyses into a comprehensive, non-redundant genomic dataset for downstream metagenomic studies.
Yes, Snakemake is required to run the metagenomic analysis workflow. It manages the underlying pipeline execution for assembly, binning, annotation, and dereplication, coordinating all dependent bioinformatics tools efficiently.
The best way to process metagenomic reads and extract MAGs is to use a pipeline that performs quality control and assembly first, then uses multiple binning algorithms like Rosella, MetaBAT2, SemiBin2, and VAMB to extract MAGs from the final contigs.
TianGzlabAlign FASTQ reads to reference genomes with BWA-MEM, Bowtie2, and Minimap2.
Zeyuyang-0420Automate manipulation, analysis, and visualization of Newick phylogenetic trees using Python's ete3 library.
nahisahoReconstruct metagenome-assembled genomes from metagenomic data with binning, quality assessment, taxonomy, dereplication, and annotation.
TianGzlabAssemble genomes de novo with SPAdes, Megahit, Flye, or Canu and report N50, N90, and GC content.