Aviary

A snakemake pipeline for binning metagenomic assemblies

Installation

git clone https://github.com/rhysnewell/aviary.git
cd aviary
conda env create -n aviary -f aviary.yml
conda activate aviary
pip install --editable .
aviary recover --help

Requirements

Initial requirements for aviary can be downloaded using the aviary.yml:

conda env create -n aviary -f aviary.yml

Usage

To perform mag recovery:

aviary recover --assembly scaffolds.fasta --short_reads_1 sr1.1.fq sr2.1.fq.gz --short_reads_2 sr1.2.fq sr2.2.fq.gz --longreads nanopore.fastq.gz --output output_dir/ --max_threads 24 --n_cores 24 --gtdb_path /path/to/gtdb/release/

Batch Files

Instead of providing aviary with an assembly and reads, you can provide it a batch file in the following format:

/Absolute/Path/to/Assembly1.fasta    Unique_ID_1    /absolute/path/to/read_set_1.1.fq.gz    /absolute/path/to/read_set_1.2.fq.gz    /absolute/path/to/read_set_2.1.fq.gz    /absolute/path/to/read_set_2.2.fq.gz
/Absolute/Path/to/Assembly2.fasta    Unique_ID_2    /absolute/path/to/read_set_3.1.fq.gz    /absolute/path/to/read_set_3.2.fq.gz    /absolute/path/to/read_set_4.1.fq.gz    /absolute/path/to/read_set_4.2.fq.gz

Then specify the path to your batch file in the config.yaml, ignoring inputs for fasta and any reads, and use the following command: snakemake --use-conda --cores 24 run_batch