List of sample identifiers from ATB deduplicated at varying levels of identity based on nucleotide sequence using sketchlib v0.2.4.
Sketching and distance calculation conducted with below commands
sketchlib sketch -f ${infile} -o ${outpref} --k-vals 21 -s 10000 --threads 11
sketchlib dist ${outpref} -k 21 --ani --threads 11 -o ${outpref}_dists.tsv
Where infile is a set of genome inputs in the format:
GENOME000001 /path/to/GENOME000001.fasta
GENOME000002 /path/to/GENOME000002.fasta… See the full description on the dataset page:
https://huggingface.co/datasets/AllTheBacteria/ATB-representative-ids.
