High-quality reference genome assembly

To obtain a representative, high-quality reference genome for short-read mapping, S. Concord isolate ITM_8091960 was sequenced using the PacBio RSII system (Pacific Biosciences, California, USA). This isolate originated from a stool sample of an Ethiopian child that presented at the travel clinic of ITM Antwerp in 2008. DNA was prepared using the PacBio Template Prep Kit (Pacific Biosciences, California, USA) and the BluePippin™ system for size selection, for sequencing with the PacBio RSII system at the Wellcome Sanger Institute (Hinxton, UK). Reads were assembled de novo using the HGAP^{56 (link)} protocol v3.0 implemented in smrtanalysis v2.3.0, resulting in one chromosome-sized contig, and five small contigs. Circlator^{57 (link)} v1.5.5 was used to remove self-compatible ends and rearrange the start positions of the contigs at the dnaA gene, or a predicted gene. The resulting contigs were polished twice using Quiver^{56 (link)}.