Otb: an Automated HiC/HiFi Pipeline Assembles the Prosapia Bicincta Genome

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2024 Jun 11

PMID 38861413

Authors

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

Affiliations

Soon will be listed here.

Abstract

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.

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