AllTheBacteria/All-representative-ids

List of sample identifiers from ATB, GTDB, MGnify, SPIRE, mOTUs and HRGM datasets, deduplicated at varying levels of identity based on nucleotide sequence using sketchlib v0.2.5.

Sketching and distance calculation conducted with below commands

sketchlib inverted build -o ${outpref} -k 21 -s 10 -f ${infile} --threads 47 --write-skq
sketchlib sketch -f ${infile} -o ${outpref} --k-vals 21 -s 1000 --threads 47

sketchlib inverted precluster --knn 50 --skd ${outpref} --ani --threads 47 -o ${outpref}_dists.tsv ${outpref}.ski

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 1 --workflow reps_graph --threshold 0.80,0.85,0.90,0.95,0.98,0.99,1.0 --outpref ${outpref} --workflow reps