AllTheBacteria/ATB-representative-ids

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
GENOME000003	/path/to/GENOME000003.fasta

Representatives were then generated using the get_representatives.py script:

python get_representatives.py --infile ${outpref}_dists.tsv --min-return 100000 --threshold 0.80,0.85,0.90,0.95,0.98,0.99,1.0 --outpref ${outpref} --workflow reps