Computational protocol: Daptomycin Resistance in Clinical MRSA Strains Is Associated with a High Biological Fitness Cost

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Protocol publication

[…] All S. aureus strains of the ST5 MLST type were downloaded from PATRIC in April, 2017 (). Strains with a BioSample identifier that unambiguously linked to a single run accession were downloaded from the European Nucleotide Archive (). When read files were paired-end, only one set in the pair was used for the comparison. Reads were aligned against N315 (PATRIC ID: 158879.11) and analyzed using the PATRIC variation service (), which uses BWA-MEM as the read aligner and FreeBayes as the SNP caller. A SNP alignment was generated by using a method previously described (). A tree for the alignment was generated using FastTree. Genes for the RNA polymerase beta-prime subunit (rpoC) were downloaded from PATRIC in April, 2017. Genes were aligned using MAFFT and a tree was built using FastTree. Trees were rendered using the iTOL website (). […]

Pipeline specifications

Software tools BWA, FreeBayes, FastTree, MAFFT, iTOL
Databases BioSample ENA PATRIC
Application Phylogenetics
Organisms Homo sapiens
Diseases Infection, Staphylococcal Infections
Chemicals Vancomycin, Daptomycin