pbptyper

pbptyper

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In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies

Documentation : https://github.com/rpetit3/pbptyper

Citation :

Directory tree:

pbptyper/
├── pbptyper_summary.tsv
├── sample-1A.tblastn.tsv
├── sample-2B.tblastn.tsv
├── sample-2X.tblastn.tsv
├── sample.fastani.tsv
└── sample.tsv

Example file for an individual sample (sample.tsv)

sample	pbptype	ani	1A_coverage	1A_pident	1A_bitscore	2B_coverage	2B_pident	2B_bitscore	2X_coverage	2X_pident	2X_bitscore	comment
streppneumo_GCA_000221985.1	NEW:626:131	94.42	100	99.278	572	100	100.000	568	100	100.000	741	

Example file for a run (pbptyper_summary.tsv)

(base) [eriny@localhost grandeur_one_of_each]$ cat pbptyper/pbptyper_summary.tsv 
sample	pbptype	ani	1A_coverage	1A_pident	1A_bitscore	2B_coverage	2B_pident	2B_bitscore	2X_coverage	2X_pident	2X_bitscore	comment
streppneumo_GCA_000221985.1	NEW:626:131	94.42	100	99.278	572	100	100.000	568	100	100.000	741	
streppneumo_GCA_002076835.1	281:348:NEW	98.34	100	100.000	573	100	100.000	567	100	96.369	718