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--- |
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license: mit |
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--- |
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List of sample identifiers from [ATB](https://allthebacteria.org), [GTDB](https://gtdb.ecogenomic.org), [MGnify](https://www.ebi.ac.uk/metagenomics), [SPIRE](https://spire.embl.de), [mOTUs](https://motus-db.org) and [HRGM](https://www.decodebiome.org/HRGM2/) datasets, deduplicated at varying levels of identity based on nucleotide sequence using [sketchlib](https://docs.rs/sketchlib/latest/sketchlib/) v0.2.4. |
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Sketching and distance calculation conducted with below commands |
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``` |
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sketchlib inverted build -o ${outpref} -k 21 -s 10 -f ${infile} --threads 47 --write-skq |
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sketchlib sketch -f ${infile} -o ${outpref} --k-vals 21 -s 1000 --threads 47 |
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sketchlib inverted precluster --knn 50 --skd ${outpref} --ani --threads 47 -o ${outpref}_dists.tsv ${outpref}.ski |
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``` |
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Where `infile` is a set of genome inputs in the format: |
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``` |
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GENOME000001 /path/to/GENOME000001.fasta |
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GENOME000002 /path/to/GENOME000002.fasta |
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GENOME000003 /path/to/GENOME000003.fasta |
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``` |
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