ena-STUDY-SC-17-12-2018-09:49:02:935-136
Anabas testudineus (climbing perch) genome assembly, primary haplotype, fAnaTes1.2
This project provides the Vertebrate Genomes Project genome assembly of Anabas testudineus, common name climbing perch, based on a sample provided by Byrappa Venkatesh. The assembly fAnaTes1.2 is based on ~68x PacBio Sequel data, ~114x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory and ~170x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip. The primary contigs were then scaffolded using the 10X data with scaff10x and mis-joins broken using break10x. 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 data and Arima Hi-C data. This was the initial fAnaTes1.1 assembly. A updated fAnaTest1.2 assembly has been further curated to removed duplicate haplotypes using purge_haplotigs and using the Hi-C data to 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 policy (https://genome10k.soe.ucsc.edu/about/data_use_policy).
This project provides the Vertebrate Genomes Project genome assembly of Anabas testudineus, common name climbing perch, based on a sample provided by Byrappa Venkatesh. The assembly fAnaTes1.2 is based on ~68x PacBio Sequel data, ~114x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute as well as BioNano Saphyr DLE data generated at the Rockefeller University Vertebrate Genome Laboratory and ~170x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip. The primary contigs were then scaffolded using the 10X data with scaff10x and mis-joins broken using break10x. 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 data and Arima Hi-C data. This was the initial fAnaTes1.1 assembly. A updated fAnaTest1.2 assembly has been further curated to removed duplicate haplotypes using purge_haplotigs and using the Hi-C data to 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 policy (https://genome10k.soe.ucsc.edu/about/data_use_policy).