| --- |
| 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 |
| |
