---
license: mit
---
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/) v0.2.5.

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](https://github.com/samhorsfield96/BacCorpusWF/blob/main/scripts/get_representatives.py) script:

```
python get_representatives.py --infile ${outpref}_dists.tsv --min-return 1 --workflow reps_graph --to-keep qc_list.csv --threshold 0.80,0.85,0.90,0.95,0.98,0.99,1.0 --outpref ${outpref} --workflow reps
```

Where qc_list.csv is set of sample ids (one per line) which passed QC measures:
- CheckM2 completeness of >=50%
- CheckM2 contamination of < 10%
- Quality score of >=50, calculated as completeness minus five times contamination
- <= 1,000 contigs
- Between 250 kb and 20 Mb in length
- Between 500 and 1,500 proteins/Mb