title: WGS of Cryptosporidium parvum
design: An aliquot of the 123 faecal isolates was used to extract genomic DNA and to identify the species and the gp60 subtype, using previously published protocols (U. Ryan et al. 2003; Alves et al. 2003). The procedures for DNA purification and extraction are detailed in Corsi et al. (Corsi et al. 2023). In short, oocyst were purified from faecal specimens by immunomagnetic separation, treated with bleach and used for genomic DNA extraction. Genomic DNA was subjected to whole genome amplification (WGA) using the REPLI-g Midi-Kit (Qiagen), according to the manufacturer's instructions. For Next Generation Sequencing experiments, about 1 g of purified WGA product per sample was used to generate Illumina Nextera XT 2 x 150 bp paired-end libraries, which were sequenced on an Illumina NovaSeq 6000 SP platform. Library preparation and sequencing were performed at the ICM (Institut du Cerveau) in Paris, France.