ena-STUDY-SC-05-03-2019-14:36:51:762-127
Mastacembelus armatus (zig-zag eel)
This project provides the genome assembly of Mastacembelus armatus, common name zig-zag eel, based on a sample provided by Byrappa Venkatesh. The assembly fMasArm1.2 is based on ~52x PacBio Sequel data, ~99x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute, as well as two-enzyme BioNano Saphyr data generated at the Rockefeller University Vertebrate Genome Laboratory and ~245x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. 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). 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. Finally, the assembly was further manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano and Arima Hi-C data. This was the fMasArm1.1 assembly. A updated fMasArm1.2 assembly has been further curated using the Hi-C data to separate out haplotigs, identify further breaks and joins and produce chromosomal-level scaffolds. Chromosomes have been 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 Mastacembelus armatus, common name zig-zag eel, based on a sample provided by Byrappa Venkatesh. The assembly fMasArm1.2 is based on ~52x PacBio Sequel data, ~99x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute, as well as two-enzyme BioNano Saphyr data generated at the Rockefeller University Vertebrate Genome Laboratory and ~245x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. 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). 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. Finally, the assembly was further manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano and Arima Hi-C data. This was the fMasArm1.1 assembly. A updated fMasArm1.2 assembly has been further curated using the Hi-C data to separate out haplotigs, identify further breaks and joins and produce chromosomal-level scaffolds. Chromosomes have been 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).