ArticleG3 (Bethesda, Md.)2024
otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome.
David C Molik, Amanda R Stahlke, Sharu P Sharma, Tyler J Simmonds, Renee L Corpuz, Angela N Kauwe, Jeremy E Schrader, Charles J Mason, Sheina B Sim, Scott M Geib
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In one paragraphArticle in G3 (Bethesda, Md.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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10 authors.
David C MolikArthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502, USA.ORCID 0000-0003-3192-6538 Amanda R StahlkeDepartment of Biological Sciences, Wubben Hall and Science Center, Colorado Mesa University, 1100 North Avenue, Grand Junction, CO 81501-3122, USA.ORCID 0000-0001-5724-598X Sharu P SharmaGenome Informatics Facility, Iowa State University, 2200 Osborn Drive, Ames, IA 50011-4009, USA.ORCID 0000-0002-6785-7071 Tyler J SimmondsTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0002-9703-5140 Renee L CorpuzTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0009-0005-6600-0788 Angela N KauweTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0003-3505-7472 Jeremy E SchraderTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0002-7013-2346 Charles J MasonTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0002-9205-8511 Sheina B SimTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0003-0914-6914 Scott M GeibTropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA.ORCID 0000-0002-9511-5139 Funding
SCINetTropical Pest Genetics and Molecular Biology Research Unit 2040-22430-028-000DUSDA Agricultural Research Service
6 · The paper itselfAbstract
The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The 2-lined spittlebug, (Prosapia bicincta, Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The 2-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.
Indexed as
Genome, InsectGenomicsAnimalsHemipteraSoftwareassembly error correctiongenome assemblyhaplotype phasingnext-generation sequencingnonmodel organism
Identifiers
PMID38861413
PMCPMC11304988
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