Computational protocol: Population Structure of Streptococcus pneumoniae Causing Invasive Disease in Adults in Portugal before PCV13 Availability for Adults: 2008-2011

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Protocol publication

[…] MLST was performed as described previously []. The DNA sequences were analyzed using Bionumerics software (Applied-Maths, Sint-Martens-Laten, Belgium) and the alleles and sequence types were assigned according to the pneumococcal MLST database available at http://pubmlst.org/spneumoniae/. The goeBURST algorithm [] implemented in the PHYLOViZ software [] was used to establish relationships between STs. Clonal complexes were defined at the single-locus-variant (SLV) and double-locus-variant (DLV) levels. […]

Pipeline specifications

Software tools BioNumerics, BURST, PHYLOViZ
Databases PubMLST
Applications Phylogenetics, WGS analysis
Organisms Streptococcus pneumoniae, Homo sapiens