ena-STUDY-SC-09-01-2018-15:09:24:920-1403
Lake Malawi cichlid Astatotilapia calliptera genome assembly fAstCal1.2
The Vertebrate Genomes Project at the Sanger Institute and the University of Cambridge, UK provides high quality reference genome assemblies for fish, caecilians and rodents as part of the Genome10K initiative. This project provides the genome assembly of the Lake Malawi cichlid Astatotilapia calliptera (Eastern Happy) as a reference for the investigation of adaptive radiation in African cichlids [PMID: 26680190]. The assembly fAstCal1.2 is based on ~75x PacBio RSII data, ~100x Illumina HiSeqX data generated from a 10X Genomics Chromium library and single-enzyme BioNano Irys data. 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. After using the PacBio data to gap fill with PBJelly and polish with Quiver, the assembly was manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano data. The assembly was then polished again using the 10X Illumina data and freebayes, and submitted as fAstCal1.1. This new assembly version fAstCal1.2 has made use of two genetic maps [PMID: 23622422, 25156298] to allocate scaffolds to chromosomes, which was followed by further curation and verification using gEVAL.
The Vertebrate Genomes Project at the Sanger Institute and the University of Cambridge, UK provides high quality reference genome assemblies for fish, caecilians and rodents as part of the Genome10K initiative. This project provides the genome assembly of the Lake Malawi cichlid Astatotilapia calliptera (Eastern Happy) as a reference for the investigation of adaptive radiation in African cichlids [PMID: 26680190]. The assembly fAstCal1.2 is based on ~75x PacBio RSII data, ~100x Illumina HiSeqX data generated from a 10X Genomics Chromium library and single-enzyme BioNano Irys data. 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. After using the PacBio data to gap fill with PBJelly and polish with Quiver, the assembly was manually curated using gEVAL to correct mis-joins and improve concordance with the BioNano data. The assembly was then polished again using the 10X Illumina data and freebayes, and submitted as fAstCal1.1. This new assembly version fAstCal1.2 has made use of two genetic maps [PMID: 23622422, 25156298] to allocate scaffolds to chromosomes, which was followed by further curation and verification using gEVAL.