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The DNA used in the Labrador assembly was derived from a male Labrador retriever. DNA long reads were generated by Novogene using a Pacific Biosciences (PacBio) Sequel instrument. Eighteen SMRT cells yielded 135 subreads (56.5x estimated raw coverage, N50 ... average=19,332). The long read data were processed at The Roslin Institute (University of Edinburgh, UK). Contig level assembly was generated using Falcon-unzip capturing the 2.4 Gbp long genome in 1,439 contigs (with contig N50 of 9Mbp). Scaffolding was done, first, using optical mapping data produced on a Bionano Saphyr instrument, University of Nottingham Deep Seq) using Bionano Solve software. This was followed by scaffolding based on proximity ligation method. The Hi-C library was created using Dovetail's Hi-C library preparation kit. Refining the scaffolds were done using Dovetail HiRise pipeline. Error correction was done using the PacBio long-read data with Racon, followed by polishing with Pilon using an Illumina short read library generated from the same dog. Gap filling was done using PBJelly with the PacBio long-read dataset.
The mitochondrial (MT) sequence was assembled from filtered, MT specific, PacBio long-read data using the Flye assembler and was error corrected with Illumina short-read data with Pilon.
Funding sources: The Dogs Trust (Experienced Investigator award to Jeffrey Schoenebeck, Emily Clark, and Alan Archibald), BBSRC ISP1 (BBS/E/D/10002070), BBSRC Responsive Mode (BB/S02008X/ Alan Archibald).
Long read DNA sequencing: Novogene, HK
Short read DNA sequencing: Novogene, HK; Edinburgh Genomics (University of Edinburgh, UK)
Optical Mapping: Deep Seq, University of Nottingham, UK
Proximity ligation-based scaffolding: Dovetail Genomics, Scotts Valley, CA 95066, United States
Sequence assembly and data integration - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK  more

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