Hybrid Genome Assembly Workflow

Quality-checked ONT reads were error-corrected using Illumina PE reads. For error correction, the Illumina PE reads were aligned to the ONT reads using BWA aligner (BWA, RRID:SCR_010910) [16 (link)]. PE reads were assembled using Abyss (ABySS, RRID:SCR_010709) [17 (link)], followed by contig extension using ONT reads using SSPACE-LongRead [18 (link)]. Super-scaffolding of the assembled scaffold was performed using SSPACE (SSPACE, RRID:SCR_005056) [19 (link)] and PLATANUS on the ONT and mate-pair data. A final draft genome resulted after gap closure using GAPCLOSER (GAPCLOSER, RRID:SCR_015026) [20 (link)] and the PLATANUS gap_close tool, with Illumina data. The genome size was estimated with a k-mer distribution plot using JELLYFISH (Jellyfish, RRID:SCR_005491) [21 (link)]. The assembly and annotation workflow is shown in Fig. 2.