Hordeum vulgare subsp. vulgare cultivar 'Morex' assembly (ONT reads with Smart denovo)

Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial compute resources and often several complementary sequencing and mapping approaches. The recent development of fast and accurate long-read sequence assembly by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies. The smartdenovo assembly was polished with ONT raw reads and PE450 Illumina short-reads of Monat et al. (2019). The wtpoa-cns module of wtdbg2 (Ruan and Li, 2020) was used for iterative polishing. Onee round of polishing with ONT reads was followed by three rounds of short-read polishing. ONT and corrected PE450 reads were aligned to the iteratively corrected assemblies with Minimap2 (Li, 2018) and alignments processed as described for CLR_wtdbg2. Sequences were provided by the University of Saskatchewan.