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IDs: 9982011 [UID] 25913928 [GenBank] 26470758 [RefSeq]
The assembly bAquChr1.4 is based on 60x PacBio data, 54x coverage 10X Genomics Chromium data, and 63x coverage Dovetail Hi-C data generated at the Wellcome Sanger Institute, and BioNano data generated by the DeepSeq facility at the University of ... Nottingham. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. As a result of the Hi-C data being sourced from a male bird it has not been possible to fully construct the W Chromosome for the female sample bAquChr1. Scaffolds identified as belonging to W have therefore been submitted as unordered fragments. The largest of these fragments has been designated as the W chromosome (SUPER_W) and all other W scaffolds labelled as W_unloc. more
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