Phylogenetic analysis of Campylobacter spp. from Botswana.

Libraries for Illumina sequencing were prepared using the NEBNext Ultra II DNA library prep kit (New England Biolabs) The genomic DNA was sheared to ~450 bp fragments in microTUBE screw-cap tubes in a M220 focused-ultrasonicator (Covaris). The sequencing library size was determined with a Bioanalyzer 2100 (Agilent) and the DNA concentration was measured with the Qubit dsDNA BR kit (Life Technologies), and pooled at equimolar amounts. The libraries were sequenced using 150 bp paired-end sequencing on the Illumina HiSeq 4000 platform (Genomics core facility at Cancer Research UK) or on the MiSeq platform with 250 or 300 bp paired-end sequencing. The Illumina HiSeq4000 read files were demultiplexed using the demuxFQ tool (Cancer Research UK) and adapter-trimmed in Cutadapt.