ena-STUDY-SC-10-05-2018-11:53:24:073-1838
Lake Tanganyika cichlid Simochromis diagramma genome assembly fSimDia1.1
The Vertebrate Genomes Project at the Sanger Institute and the University of Cambridge, UK provides high quality reference genome assemblies for fish, caecilians and rodents as part of the Genome10K initiative. This project provides the genome assembly of Simochromis diagramma. The assembly fSimDia1.1 is based on ~69x PacBio Sequel data, and ~54x Illumina HiSeqX data generated from a 10X Genomics Chromium library. An initial PacBio assembly was made using Falcon-unzip and the primary contigs extended by merging with a miniasm assembly. The contigs were then scaffolded using the 10X data with scaff10x, and using synteny with Lates calcarifer (Asian seabass) with cross_genome. After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the 10X Illumina data and freebayes. Retained haplotigs were identified with purge_haplotigs. Finally, the assembly was manually improved using gEVAL.
The Vertebrate Genomes Project at the Sanger Institute and the University of Cambridge, UK provides high quality reference genome assemblies for fish, caecilians and rodents as part of the Genome10K initiative. This project provides the genome assembly of Simochromis diagramma. The assembly fSimDia1.1 is based on ~69x PacBio Sequel data, and ~54x Illumina HiSeqX data generated from a 10X Genomics Chromium library. An initial PacBio assembly was made using Falcon-unzip and the primary contigs extended by merging with a miniasm assembly. The contigs were then scaffolded using the 10X data with scaff10x, and using synteny with Lates calcarifer (Asian seabass) with cross_genome. After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the 10X Illumina data and freebayes. Retained haplotigs were identified with purge_haplotigs. Finally, the assembly was manually improved using gEVAL.