otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome

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David 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


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 Two-lined spittlebug Prosapia bicincta, (Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. This insect is a significant threat to grasslands and pastures, leading to wilting and phytotoxemia when feeding, ultimately resulting in plant mortality. 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. The two-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera.




Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences


HiFi, HiC, Assembly Pipeline, Computational Biology, Genomic Assembly, Hemiptera, Cercopidae, Nextflow, Singularity


Published: 2023-12-05 17:32

Last Updated: 2023-12-06 03:12

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Data and Code Availability Statement:
Code used in the creation of this genome is in the public domain per United States 17 U.S.C. § 105. The code is freely available for use and modification: https://github.com/molikd/otb , https://github.com/molikd/Shhquis.jl Data published for this article are in the public domain per United States 17 U.S.C. § 105. The data are freely available for use and modification: https://www.ncbi.nlm.nih.gov/bioproject/987615, https://www.ncbi.nlm.nih.gov/biosample/SAMN35984262