ena-STUDY-SC-14-12-2018-15:01:46:984-73
Gouania willdenowi (blunt-nosed clingfish)
This project provides the Vertebrate Genomes Project genome assembly of Gouania willdenowi, common name blunt-nosed clingfish, based on a sample provided by Hannes Svardal. The assembly fGouWil2.1 is based on ~58x PacBio Sequel data, ~67x coverage Illumina HiSeqX data from a 10X Genomics Chromium library and two-enzyme BioNano Irys data generated at the Wellcome Sanger Institute as well as ~83x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. The assembly was made using the Vertebrate Genomes Project v1.5 assembly pipeline on DNAnexus. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further with BioNano hybrid scaffolding and scaffolded further still using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano and 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 Gouania willdenowi, common name blunt-nosed clingfish, based on a sample provided by Hannes Svardal. The assembly fGouWil2.1 is based on ~58x PacBio Sequel data, ~67x coverage Illumina HiSeqX data from a 10X Genomics Chromium library and two-enzyme BioNano Irys data generated at the Wellcome Sanger Institute as well as ~83x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. The assembly was made using the Vertebrate Genomes Project v1.5 assembly pipeline on DNAnexus. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further with BioNano hybrid scaffolding and scaffolded further still using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano and 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).