Enhancing Genomic Assembly Accuracy Through Hybrid In Silico Library and Reference-Guided Misassembly Correction

After co-assembly of the draft genomes for Megalobrama amblycephala (GCA_009869865.1) and Culter alburnus (GCA_009869775.1, GCA_028476615.1) using the reference-guided assemblers Ragout v2.3 and Ragtag v2.1, we utilized Culter erythropterus (GCA_024489055.1), C. alburnus (GWHBOSX00000000), and M. amblycephala (GCA_018812025.1) as reference genomes. We employed the Ragtag Correct function along with an in silico paired-end 500 bp library to rectify misassemblies in the target genomes of M. amblycephala (GCA_009869865.1) and C. alburnus (GCA_009869775.1, GCA_028476615.1). This process yielded improved versions of the three genomic drafts designated cor_ma, cor_ca, and cor_ca_hu, respectively.