Fully resolved assembly of Cryptosporidium parvum

Background Cryptosporidium parvum are apicomplexan parasites commonly found across many species with a global infection prevalence of 7.6%. As such it is important to understand the diversity and genomic makeup of this prevalent parasite to prohibit further spread and to fight an infection. The general basis of every genomic study is a high quality reference genome that has continuity and completeness, and is of high quality and thus enables comprehensive comparative studies. Findings Here we provide a highly accurate and complete reference genome of Cryptosporidium spp.. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall the assembly shows a high completion rate with 98.4% single copy Busco genes. This is also shown by the identification of 13 telomeric regions across the 8 chromosomes. The consensus accuracy of the established reference genome was further validated by sequence alignment of established genetic markers for C.parvum. Conclusions This high quality reference genome provides the basis for subsequent studies and comparative genomic studies across the Cryptosporidium clade.