Skip to content

Latest commit

 

History

History
32 lines (14 loc) · 1.51 KB

readme.md

File metadata and controls

32 lines (14 loc) · 1.51 KB

Streptococcus pneumoniae RASE database

Dataset

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.

Methods

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.

Issues

Please use Github issues.

Releases and changelog

See Github releases.

License

MIT.

Contact

Karel Brinda <[email protected]>