Culex Johannesburg Genome sequencing and assembly

Culex quinquefasciatus is a major vector of West Nile virus, which is now the leading cause of mosquito-borne disease in the continental US. The JHB strain of Culex quinquefasciatus, the strain from which previous genome assemblies were derived, maintained high heterozygosity, which presented a challenge to obtaining a high-quality reference assembly. In this project we obtained long Oxford Nanopore (ONT) sequences from F1 male siblings and separated them into paternal and maternal reads by TrioCanu according to paternal-specific and maternal-specific k-mers identified from the paternal and maternal Illumina reads (F0 father and mother, ~100x coverage each). All paternal-specific reads plus unseparated reads were used to obtain a paternal assembly by Canu and then polished using the F0 Illumina reads by Pilon. The assembly was further scaffolded using a Bionano optical map and HiC.