Main tool : pbptyper
Full documentation: https://github.com/rpetit3/pbptyper
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
# run pbptyper on an test S. pneumo assembly included with pbptyper
# WARNING: test data no longer included in docker image, visit here to get test data: https://github.com/rpetit3/pbptyper/tree/main/test
$ pbptyper --input SRR2912551.fna.gz --prefix SRR2912551 --db /pbptyper-*/db/ --outdir /SRR2912551-pbptyper-test
Running TBLASTN for 1A...
TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-1A.tblastn.tsv
Running TBLASTN for 2B...
TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2B.tblastn.tsv
Running TBLASTN for 2X...
TBLASTN results written to /SRR2912551-pbptyper-test/SRR2912551-2X.tblastn.tsv
Predicted PBP Type
┏━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━┓
┃ sample ┃ pbptype ┃ 1A_coverage ┃ 1A_pident ┃ 2B_coverage ┃ 2B_pident ┃ 2X_coverage ┃ 2X_pident ┃
┡━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━┩
│ SRR2912551 │ 23:0:2 │ 100 │ 100.000 │ 100 │ 100.000 │ 100 │ 100.000 │
└────────────┴─────────┴─────────────┴───────────┴─────────────┴───────────┴─────────────┴───────────┘
Predicted pbp type result written to /SRR2912551-pbptyper-test/SRR2912551.tsv