Package: aviary-genome
AviaryAn easy to use for wrapper for a robust snakemake pipeline for metagenomic short-read, long-read, and hybrid assembly.
Aviary also performs binning, annotation, strain diversity analyses,a nd provides users with an easy way to combine and
dereplicate many aviary results with rapidity. The pipeline currently includes a series of distinct, yet flexible, modules
that can seamlessly communicate with each other. Each module can be run independently or as a single pipeline depending on provided input.Please refer to the full docs hereQuick InstallationYour conda channels should be configured ideally in this order:conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forgeYour resulting.condarcfile should look something like:channels:
  - conda-forge
  - bioconda
  - defaultsOption 1: Install from BiocondaConda can handle the creation of the environment for you directly:conda create -n aviary -c bioconda aviaryOr install into existing environment:conda install -c bioconda aviaryOption 2: Install from pipCreate the environment using theaviary.ymlfile then install from pip:conda env create -n aviary -f aviary.yml
conda activate aviary
pip install aviary-genomeOption 3: Install from sourceInitial requirements for aviary can be downloaded using theaviary.yml:git clone https://github.com/rhysnewell/aviary.git
cd aviary
conda env create -n aviary -f aviary.yml
conda activate aviary
pip install -e .Whatever option you choose, runningaviary --helpshould return the following
output:......:::::: AVIARY ::::::......

           A comprehensive metagenomics bioinformatics pipeline

Metagenome assembly, binning, and annotation:
        assemble  - Perform hybrid assembly using short and long reads, 
                    or assembly using only short reads
        recover   - Recover MAGs from provided assembly using a variety 
                    of binning algorithms 
        annotate  - Annotate MAGs using EggNOG and GTBD-tk
        genotype  - Perform strain diversity analysis of MAGs using Lorikeet
        complete  - Runs each stage of the pipeline: assemble, recover, 
                    annotate, genotype in that order.
        cluster   - Combines and dereplicates the MAGs from multiple Aviary runs
                    using Galah

Isolate assembly, binning, and annotation:
        isolate   - Perform isolate assembly **PARTIALLY COMPLETED**
        
Utility modules:
        configure - Set or overwrite the environment variables for future runs.Upon first running aviary you will be prompted to input the location for where you would like
your conda environments to be stored, the GTDB release installed on your system, the location of your
EnrichM database, and the location of your BUSCO database. These locations will be stored as environment
variables, but for aviary to be able to use those environment variables you will have to either source your .bashrc
or reactivate your conda environment depending on whether you installed aviary within a conda environment or not:conda deactivate; conda activate aviary

OR

source ~/.bashrcThese environment variables can be reset usingaviary configureDatabasesAviary uses programs which require access to locally stored databases.
These databases can be quite large, as such we recommend setting up one instance of Aviary and these databases per machine or machine cluster.Therequireddatabases are as follows:GTDBEggNogCheckM2Installing databasesAviary can handle the download and installation of these databases via use of the--downloadflag. Using--downloadwill download and install the databases into the folders corresponding to their associated environment variables. Aviary will
ask you to set these environment variables upon first running and if they are not already available. Otherwise, users can use
theaviary configuresubcommand to reset the environment variables:aviary configure -o logs/ --eggnog-db-path /shared/db/eggnog/ --gtdb-path /shared/db/gtdb/ --checkm2-db-path /shared/db/checkm2db/ --downloadThis command will check if the databases exist at those given locations, if they don't then aviary will download and change
the conda environment variables to match those paths.N.B.Again, these databases are VERY large. Please talk to your sysadmin/bioinformatics specialist about setting a shared
location to install these databases to prevent unnecessary storage use. Additionally, the--downloadflag can be used within
any aviary module to check that databases are configured properly.Environment variablesUpon first running Aviary, you will be prompted to input the location for several database folders if
they haven't already been provided. If at any point the location of these folders change you can
use the theaviary configuremodule to update the environment variables used by aviary.These environment variables can also be configured manually, just set the following variables in your.bashrcfile:export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release207/db/ # https://gtdb.ecogenomic.org/downloads
export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.8/ # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup
export CHECKM2DB=/path/to/checkm2db/
export CONDA_ENV_PATH=/path/to/conda/envs/WorkflowCitationsIf you use aviary then please be aware that you are using a great number of other programs and aviary wrapping around them.
You should cite all of these tools as well, or whichever tools you know that you are using. To make this easy for you
we have provided the following list of citations for you to use in alphabetical order. This list will be updated as new
modules are added to aviary.A constantly updating list of citations can be found in theCitations document.LicenseCode isGPL-3.0