{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Rayamajhi N"],"funding":["NSF OPP"],"pagination":["jkac192"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9635638"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["12(11)"],"pubmed_abstract":["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 3 phases: (1) short-read only, (2) short- and long-read hybrid, and (3) long-read only assemblies. Each of the phases has its own error model. We hypothesized that hidden short-read scaffolding errors and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of Trematomus borchgrevinki from data generated during each of the 3 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-"],"journal":["G3 (Bethesda, Md.)"],"pubmed_title":["Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki."],"pmcid":["PMC9635638"],"funding_grant_id":["1645087"],"pubmed_authors":["Cheng CC","Rayamajhi N","Catchen JM"],"additional_accession":[]},"is_claimable":false,"name":"Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki.","description":"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 3 phases: (1) short-read only, (2) short- and long-read hybrid, and (3) long-read only assemblies. Each of the phases has its own error model. We hypothesized that hidden short-read scaffolding errors and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of Trematomus borchgrevinki from data generated during each of the 3 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-","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Nov","modification":"2026-07-16T12:38:52.921Z","creation":"2025-04-06T18:22:44.344Z"},"accession":"S-EPMC9635638","cross_references":{"pubmed":["35904764"],"doi":["10.1093/g3journal/jkac192"]}}