This is a de novo genome assembly for a single Todiramphus albicilla sample (KUNHM catalogue number 116001; http://portal.vertnet.org/o/ku/birds?id=f6469ef5-7b47-11e4-8ef3-782bcb9cd5b5). High molecular weight genomic DNA was extracted from muscle tissue at HudsonAlpha Institute for Biotechnology and prepared into a 10X Chromium sequencing library. This library was sequenced with 150 base pair (bp) paired-end reads across two lanes on an Illumina HiSeq X machine, which generated 365,992,456 linked read pairs passing initial quality filters. The resulting sequence data were assembled de novo with Supernova v2.1 (Weisenfeld, Kumar, Shah, Church, & Jaffe, 2017). De novo assembly of all linked read pairs sequenced from our 10X Chromium sequencing library generated an initial phased genome assembly comprising 28,857 contigs contained in 10,881 total scaffolds, with an overall length of 1.15 gigabases (Gb), and 1.6% of the overall assembly comprised of N's (missing base calls). Contiguity metrics revealed a contig N50 = 126.7 kilobases (Kb), and a scaffold N50 = 4.69 megabases (Mb) for this de novo assembly, suggesting that the relatively short contigs we recovered were effectively linked into moderate to large sized scaffolds (largest scaffold = 20.9 Mb) via the long-range linkage information afforded by this linked read approach. A BUSCO analysis revealed that 95.9% of all expected avian orthologs were present and complete in our de novo assembly (7,999 out of 8,338 searched; 95.7% present in a single copy and 0.2% present with duplicate copies), 1.5% were present in a fragmented state, and 2.6% were completely absent. In sum, this de novo assembly is highly complete, with a reasonably low proportion of missing base calls, and is comprised of short contigs and moderately sized scaffolds.
Less...