Galah image

By David Cook Wildlife Photography - originally posted to Flickr as Galah (Eolophus roseicapillus), CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=8388233

Galah

Travis

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, 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 genome qualities were specified, then the clusters have an additional property:

  1. Each representative genome has a better quality score than other members of the cluster.

If CheckM qualities are not used, then:

  1. 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 this publication.

Installation

Galah is not currently available on bioconda, though it can (or will soon be) be installed and used indirectly through CoverM, which is available on bioconda.

Currently Galah can only be installed following the development instructions below. Hopefully soon it will be available on crates.io.

Development

To run an unreleased version of Galah, after installing Rust:

git clone https://github.com/wwood/galah cd galah cargo run -- cluster ...etc...

Dependencies

Galah relies on these 3rd party tools, which must be installed separately.

Usage

For clustering a set of genomes at 99% ANI: galah cluster --genome-fasta-files /path/to/genome1.fna /path/to/genome2.fna >clusters There are several other options for specifying genomes, ANI cutoffs, etc. See galah cluster --help for more information.

Precluster ANI

Similar to dRep, galah operates in two stages. In the first, a fast pre-clustering distance (dashing) is calculated between each pair of genomes. Genome pairs are only considered as potentially in the same cluster with 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 Australian Centre for Ecogenomics.