sourmash-oddify contains tools and workflows for examining bacterial and archaeal genome contamination with k-mers using sourmash.
Briefly, sourmash-oddify will:
- classify genomes with GTDB-Tk
- build sourmash LCA databases based on the resulting taxonomy
- identify, align, report, and ~remove taxonomically discordant sub-sequences
The primary value-add of sourmash-oddify is that it uses sourmash to quickly identify genomes that share many taxonomically discordant k-mers. These genomes can then be further investigated. (See the Kraken section in this blog post for more info on how we identify taxonomically discordant k-mers.)
sourmash-oddify is in the early stages of development but we are happy to support your using it! Please post questions and problems to our issue tracker.
You can install all of the software dependencies with bioconda by running:
conda env create -f environment.yml
The primary way to use sourmash-oddify is to run the snakemake workflow in the Snakefile. Do so by:
conf/default.ymlto a new file and editing it
snakemake --use-conda --configfile=newconf.yml
The output will be placed in the
outputs_dir specified in your config file.
More on what this output is ...later. :)
For now, your genome identifiers must have a common prefix of at least one
character. Put this prefix in the
filter_prefixes in your config file.
GTDB-Tk reference data
Since sourmash-oddify runs gtdbtk, you'll need the GTDB-Tk reference
Download it, unpack it somewhere, and then set the value for
gtdbtk_data in your config file to the unpacked directory path.
Note, this should be set to the top level directory containing the