Fantastic bees and how to assemble them: Instant ASM-Bee is a bioinformatic pipeline for assembling bee genomes and other insects

The USDA-ARS Beenome100 initiative and analogous sequencing efforts have the broad goal of sequencing and assembling genomes to contribute to our understanding of specific and broad taxa. This knowledge contributes to advancements to various fields including biology, ecology, and evolution, with applications to conservation efforts, pollinator health, and pest management strategies. Meeting these goals necessitates a robust and comprehensive bioinformatic pipeline for genome assembly and analysis. Beginning with PacBio HiFi reads and short HiC reads, Instant ASM-Bee assembles bee and insect genomes into contigs and then scaffolds the assembly using HiC contacts. Execution of the pipeline results in a chromosome-scale assembly, an annotated mitochondrial genome, repeat analysis, and exploratory metagenomic analyses using peer-reviewed and opensource software. This assembly and analysis pipeline facilitates filtering and masking for contaminants and results in an assembly ready for to public databases such as NCBI. Beyond the specific assembly programs and data types used for this pipeline, Instant ASM-Bee provides a standardized framework for assembling genomes as nucleic acid sequencing technology advances in the future to support our understanding of bees and other insects and eukaryotes.