ena-STUDY-SC-07-12-2018-13:46:49:223-320
Cottoperca gobio (channel bull blenny) genome assembly, fCotGob3.1
This project provides the Vertebrate Genomes Project genome assembly of the notothenioid fish Cottoperca gobio, common name channel bull blenny, based on a sample provided by Bill Detrich. The assembly fCotGob3.1 is based on ~75x PacBio Sequel data, and ~54x Illumina HiSeqX data generated from a 10X Genomics Chromium library obtained at the Wellcome Sanger Institute as well as BioNano Saphyr two-enzyme data generated at by BioNano and ~145x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. The Hi-C data was generated from a different individual (fCotGob2, sample SAMEA104242971) than the other genomic data. An initial PacBio assembly was made using Falcon-unzip without repeat-masking during overlap detection. The primary contigs were first scaffolded using a wtdbg assembly as a guide, then scaffolded further using the 10X data with scaff10x and then with BioNano two-enzyme hybrid scaffolding. 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. Contiguity was then further increased by filling gaps with the contigs from a wtdgb assembly made from Canu corrected PacBio reads. The assembly was then re-polished with Arrow and freebayes. Retained haplotigs were identified with purge_haplotigs. Finally, the assembly was scaffolded to chromosomes using Arima Hi-C data and manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano data and Arima Hi-C data. Chromosomes are named by synteny to medaka. The assembly is provided by the Wellcome Sanger Institute and Cambridge University team (https://www.sanger.ac.uk/science/data/vertebrate-genomes-sequencing) of the Vertebrate Genomes Project (http://vertebrategenomesproject.org). The data under this project are made available subject to the Genome10K data use policies (https://genome10k.soe.ucsc.edu/data-use-policies).
This project provides the Vertebrate Genomes Project genome assembly of the notothenioid fish Cottoperca gobio, common name channel bull blenny, based on a sample provided by Bill Detrich. The assembly fCotGob3.1 is based on ~75x PacBio Sequel data, and ~54x Illumina HiSeqX data generated from a 10X Genomics Chromium library obtained at the Wellcome Sanger Institute as well as BioNano Saphyr two-enzyme data generated at by BioNano and ~145x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. The Hi-C data was generated from a different individual (fCotGob2, sample SAMEA104242971) than the other genomic data. An initial PacBio assembly was made using Falcon-unzip without repeat-masking during overlap detection. The primary contigs were first scaffolded using a wtdbg assembly as a guide, then scaffolded further using the 10X data with scaff10x and then with BioNano two-enzyme hybrid scaffolding. 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. Contiguity was then further increased by filling gaps with the contigs from a wtdgb assembly made from Canu corrected PacBio reads. The assembly was then re-polished with Arrow and freebayes. Retained haplotigs were identified with purge_haplotigs. Finally, the assembly was scaffolded to chromosomes using Arima Hi-C data and manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano data and Arima Hi-C data. Chromosomes are named by synteny to medaka. The assembly is provided by the Wellcome Sanger Institute and Cambridge University team (https://www.sanger.ac.uk/science/data/vertebrate-genomes-sequencing) of the Vertebrate Genomes Project (http://vertebrategenomesproject.org). The data under this project are made available subject to the Genome10K data use policies (https://genome10k.soe.ucsc.edu/data-use-policies).