Anopheles coluzzii principal pseudohaplotype genome sequencing. Anopheles coluzzii

The assembly AcolN3 is based on 59x PacBio HiFi data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Anopheles Reference Genomes project. The assembly process included the following sequence of steps: initial PacBio assembly generation with hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named, ordered and oriented based on published data.