Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki

For any genome-based research, a robust genome assembly is required. De novo assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least three phases: i) short-read only, ii) short- and long-read hybrid, and iii) long-read only assemblies. Each of the phases has their own error model. We hypothesized that hidden scaffolding errors in short-read assembly and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of T. borchgrevinki from data generated during each of the three phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer-based strategy improved short-read assemblies as measured by BUSCO while mate-pair libraries introduced hidden scaffolding errors and perturbed BUSCO scores. Further, we found that al..., , , # Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki

[https://doi.org/10.5061/dryad.ghx3ffbs3](https://doi.org/10.5061/dryad.ghx3ffbs3)

Illumina based short-reead only de novo genome assembly built with kmer size 51 using Meraculous (v2.2.2.5, Chapman et al. 2011) named as k51 and the file name is k51.fasta

Illumina based short-reead only de novo genome assembly built with kmer size 61 using Meraculous (v2.2.2.5, Chapman et al. 2011) named as k61 and the file name is k61.fasta

Illumina based short-reead only de novo genome assembly built with kmer size 71 using Meraculous (v2.2.2.5, Chapman et al. 2011) named as k71 and the file name is k71.fasta

Illumina based short-reead only de novo genome assembly built with kmer size 81 using Meraculous (v2.2.2.5, Chapman et al. 2011) named as k81 and the file name is k81.fasta

Illumina based short-reead only de novo genome assembly built with kmer size 91 using Meracu...