We used 616 pneumococcal genomes from a carriage study in Massachusetts children [Croucher et al. 2013, Croucher et al. 2015]. The datasets comprises draft genome assemblies from Illumina HiSeq reads, resistance data, and lineages inferred from sequence cluster computed using BAPS.
The S. pneumoniae RASE database was constructed with the EUCAST breakpoints ([mg/L]): ceftriaxone (CRO): 0.25, erythromycin (ERY): 0.25, benzylpenicillin (PEN): 0.06, trimethoprim-sulfamethoxazole (SXT): 1.00, and tetracycline (TET): 1.00.
The draft assemblies were downloaded from the SRA FTP server using the accession codes provided in Table 1 of [Croucher et al. 2015]. The phylogenetic tree was downloaded from DataDryad. The pneumococcal ProPhyle index was constructed with the k-mer size k=18.
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