Sturnus vulgaris isolate:sv1000_unsw Genome sequencing and assembly

The European starling (Sturnus vulgaris) is an ecologically significant avian, with drastic native population declines concurrent to near global invasion success. Here, we de novo sequence the genome of an Australian individual, to provide an important genomic resource for future molecular work on this species.The S. vulgaris vAU genome assembly was produced via eight assembly steps. The 10x reads were assembled into an initial diploid assembly using SUPERNOVA (v2.1.1) with barcode fraction and reads subsample calculated following SUPERNOVA best practices (parameters: bcfrac = 0.8, maxreads = 550 million). This assembly was then split into non-redundant primary and alternative haploid assemblies using DIPLOIDOCUS (parameters: runmode= diphapnr) (V0.9.5). The primary haploid assembly produced by DIPLOIDOCUS was scaffolded using the filtered ONT reads using the program SSPACE-LONGREAD (v1-1). The filtered ONT reads were then used to gap-fill the assembly using GAPFINISHER (v1.0). Clustered high quality Iso-Seq reads were then used for a secondary round of scaffolding using L_RNA_SCAFFOLDER. Paired-end 10x linked reads were processed with 10X Genomics LONG RANGER (v2.2) and mapped onto this scaffolded assembly using BWA mem before error correction of SNPs and indels using PILON (v1.23). To validate the scaffolds, the assembly was analysed using the BREAK10X toolkit in SCAFF10X (v3.1). The assembly was further checked for assembly artefacts and contamination using DIPLOIDOCUS (parameters: runmode=purgehaplotig & runmode= vecscreen) (v0.9.5). We aligned our assembly to the chromosome scale assembly of zebra finch (Taeniopygia guttata) (NCBI= GCF_008822105.2) using SATSUMA2 to create putative chromosomes assuming orthology.