otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome

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, qua...

Full description

Saved in:
Bibliographic Details
Published in:G3 : genes - genomes - genetics 2024-08, Vol.14 (8)
Main Authors: Molik, David C, Stahlke, Amanda R, Sharma, Sharu P, Simmonds, Tyler J, Corpuz, Renee L, Kauwe, Angela N, Schrader, Jeremy E, Mason, Charles J, Sim, Sheina B, Geib, Scott M
Format: Article
Language:English
Subjects:
Animals
Genome, Insect
Genomics - methods
Hemiptera - genetics
Investigation
Software
Citations: Items that this one cites
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2160-1836
2160-1836
DOI:10.1093/g3journal/jkae129