ena-STUDY-SC-14-12-2018-16:14:44:114-98
Betta splendens (Siamese fighting fish)
This project provides the genome assembly of the gourami fish Betta splendens, common name Siamese fighting fish, based on a sample provided by Ronny Kyller. The assembly fBetSpl5.2 is based on ~48x PacBio Sequel data and ~83x coverage Illumina HiSeqX data from a single individual (fBetSpl5, sample SAMEA104381735). Scaffolding and curation also integrated ~183x Illumina HiSeqX data generated from a 10X Genomics Chromium library and single-enzyme BioNano Irys data, both from a separate individual (fBetSpl1, sample SAMEA104381745). All data was generated at the Wellcome Sanger Institute. An initial PacBio assembly of fBetSpl5 was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data from fBetSpl1 with scaff10x. After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the fBetSpl5 Illumina data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano data. By aligning with the existing Betta splendens assembly (GCA_003650155.1) and medaka, we were able to order and orient our scaffolds and place onto chromosomes. 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 genome assembly of the gourami fish Betta splendens, common name Siamese fighting fish, based on a sample provided by Ronny Kyller. The assembly fBetSpl5.2 is based on ~48x PacBio Sequel data and ~83x coverage Illumina HiSeqX data from a single individual (fBetSpl5, sample SAMEA104381735). Scaffolding and curation also integrated ~183x Illumina HiSeqX data generated from a 10X Genomics Chromium library and single-enzyme BioNano Irys data, both from a separate individual (fBetSpl1, sample SAMEA104381745). All data was generated at the Wellcome Sanger Institute. An initial PacBio assembly of fBetSpl5 was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data from fBetSpl1 with scaff10x. After using the PacBio data to gap fill with PBJelly and polish with Arrow, the assembly was polished again using the fBetSpl5 Illumina data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano data. By aligning with the existing Betta splendens assembly (GCA_003650155.1) and medaka, we were able to order and orient our scaffolds and place onto chromosomes. 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).