Main tool : pasty
Additional tools:
- camlhmp 1.0.0
- blast 2.16.0+
Full documentation: https://github.com/rpetit3/pasty
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies
pasty --input ./data/O1-GCF_001420225.fna.gz --prefix O1-GCF_001420225 --outdir results/
Running camlhmp with following parameters:
--input ./data/O1-GCF_001420225.fna.gz
--yaml /opt/conda/bin/../share/pasty/pa-osa.yaml
--targets /opt/conda/bin/../share/pasty/pa-osa.fasta
--outdir results/
--prefix O1-GCF_001420225
--min-pident 95
--min-coverage 95
Starting camlhmp for P. aeruginosa serogrouping...
Running blastn...
Processing hits...
Final Results...
P. aeruginosa serogrouping
┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┓
┃ sample ┃ type ┃ targets ┃ coverages ┃ hits ┃ schema ┃ schema_version ┃ camlhmp_version ┃ params ┃ comment ┃
┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━┩
│ O1-GCF_001420225 │ O1 │ O1 │ 100.00 │ 1 │ pasty │ 2.1.0 │ 1.0.0 │ min-coverage=95;min-pident=95 │ │
└──────────────────┴──────┴─────────┴───────────┴──────┴────────┴────────────────┴─────────────────┴───────────────────────────────┴─────────┘
Writing outputs...
Final predicted type written to results/O1-GCF_001420225.tsv
Results against each type written to results/O1-GCF_001420225.details.tsv
blastn results written to results/O1-GCF_001420225.blastn.tsv