Fig. 1
An overview of assembly methods. Contig assembly was carried out with the diploid assembler FALCON-Unzip to produce primary contigs and haplotigs. It began with selection of longest “seed” reads and shorter reads were aligned to them to create pre-assemble reads using a consensus approach. The primary contigs were carried forward to the scaffolding step that began with Chicago reads for short range scaffolding (1–100 kb) with HiRise. Then long-range scaffolding (10–10,000 kb) was carried out with Hi-C reads to cluster scaffolds to the chromosome level. Each join of contigs to create a scaffold was checked against an LD map and for conservation of synteny with cattle and goat. Then long-reads were used to fill gaps and polish the sequence, followed by indel correction with short reads
