- [Galah](#galah) - [Installation](#installation) - [Install through the bioconda package](#install-through-the-bioconda-package) - [Pre-compiled binary](#pre-compiled-binary) - [Compiling from source](#compiling-from-source) - [Development](#development) - [Dependencies](#dependencies) - [Usage](#usage) - [Precluster ANI](#precluster-ani) - [License](#license) # Galah [](https://anaconda.org/bioconda/galah) Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method. That is, it clusters microbial genomes together based on their average nucleotide identity (ANI), and chooses a single member of each cluster as the representative. Galah uses a greedy clustering approach to speed up genome dereplication, relative to e.g. [dRep](https://drep.readthedocs.io/), particularly when there are many closely related genomes (i.e. >95% ANI). Generated cluster representatives have 2 properties. If the ANI threshold was set to 99%, then: 1. Each representative is <99% ANI to each other representative. 2. All members are >=99% ANI to the representative. If [CheckM](https://ecogenomics.github.io/CheckM/) genome qualities were specified, then the clusters have an additional property: 3. Each representative genome has a better quality score than other members of the cluster. Each genome is assigned a quality score based on the formula `completeness-5*contamination-5*num_contigs/100-5*num_ambiguous_bases/100000`, which is reduced from a quality formula described in Parks et. al. 2020 https://doi.org/10.1038/s41587-020-0501-8. If instead CheckM qualities were not provided, then the following holds instead: 3. Each representative genome was specified to galah before other members of the cluster. The overall greedy clustering approach was largely inspired by the work of Donovan Parks, as described in [Parks et. al. 2020](https://doi.org/10.1038/s41587-020-0501-8). It operates in 3 steps. In the first step, genomes are assigned as representative if no genomes of higher quality are >99% ANI. In the second step, each non-representative genome is assigned to the representative genome it has the highest ANI with. ## Installation ### Install through the bioconda package Galah can be installed through the [bioconda](https://bioconda.github.io/user/install.html) conda channel. After initial setup of conda and the bioconda channel, it can be installed with mamba (or conda) with: ``` mamba install galah ``` One can see [details of the galah recipe](https://bioconda.github.io/recipes/galah/README.html). Galah can also be used indirectly through [CoverM](https://github.com/wwood/CoverM) via its `cluster` subcommand, which is also available on bioconda. ### Pre-compiled binary Galah can be installed by downloading statically compiled binaries, available on the [releases page](https://github.com/wwood/Galah/releases). Third party dependencies listed below are required for this method. ### Compiling from source Galah can also be installed from source, using the cargo build system after installing [Rust](https://www.rust-lang.org/). ``` cargo install galah ``` Third party dependencies listed below are required for this method. ### Development To run an unreleased version of Galah, after installing [Rust](https://www.rust-lang.org/): ``` git clone https://github.com/wwood/galah cd galah cargo run -- cluster ...etc... ``` Third party dependencies listed below are required for this method. ### Dependencies For some advanced usage of Galah, 3rd party tools are required, which must be installed separately: * Dashing v0.4.0 https://github.com/dnbaker/dashing * FastANI v1.31 https://github.com/ParBLiSS/FastANI ## Usage For clustering a set of genomes at 99% ANI: ``` galah cluster --genome-fasta-files /path/to/genome1.fna /path/to/genome2.fna --output-cluster-definition clusters.tsv ``` There are several other options for specifying genomes, ANI cutoffs, etc. The full usage is described on the [manual page](https://wwood.github.io/galah/galah-cluster.html), which can be accessed on the command line running `galah cluster --full-help`. ### Precluster ANI Similar to dRep, galah operates in two stages. In the first, a fast pre-clustering distance ([dashing](https://github.com/dnbaker/dashing)) is calculated between each pair of genomes. Genome pairs are only considered as potentially in the same cluster with [FastANI](https://github.com/ParBLiSS/FastANI) if the prethreshold ANI is greater than the specified value. By default, the precluster ANI is set at 95% and the final ANI is set at 99%. ## License Galah is made available under GPL3+. See LICENSE.txt for details. Copyright Ben Woodcroft. Developed by Ben Woodcroft at the [Centre for Microbiome Research, Queensland University of Technology](https://www.qut.edu.au/health/schools/school-of-biomedical-sciences/centre-for-microbiome-research). [galah]: Eolophus_roseicapilla_-Wamboin,_NSW,_Australia_-juvenile-8.smaller.jpg