Genome assembly
Genome assembly was conducted on Galaxy Australia (The Galaxy Community,
2022) following the genome assembly guide (Price & Farquharson, 2022).
HiFiAdapterFilt was used to remove adapter sequence in the raw PacBio
HiFi reads (Sim et al., 2022), followed by assembly with HiFiasm v0.16.1
with default parameters (Cheng et al., 2021; Cheng et al., 2022).
The quality of the genome assembly was assessed on Galaxy Australia with
the genome assessment post-assembly workflow (Price, 2023). Basic genome
assembly statistics were calculated with QUAST v5.0.2 (Mikheenko et al.,
2018). Completeness was assessed using Benchmarking Universal
Single-Copy Orthologs (BUSCO) v5.2.2 (Simão et al., 2015) with the
Aves_odb10 lineage (n = 8,338 BUSCOs). The repetitive elements of the
genome were identified and classified by building a custom database
using RepeatModeler v2.0.1 (Flynn et al., 2020) and RepeatMasker v4.0.9
(Smit et al., 2013-2015) with the -nolow parameter to avoid masking of
simple low-complexity repeats, run on a Pawsey Supercomputing Centre
Nimbus cloud machine (256 GB RAM, 64 vCPU, 3 TB storage).