D3156: A bioinformatic workflow for genome assembly from anchored hybrid enrichment raw sequence data of Ephemeroptera (mayflies)

Next Generation Sequencing (NGS) technologies are highly regarded as a highly accurate and cost effective method of DNA sequencing. Anchored Hybrid Enrichment (AHE) has been used across different taxonomic groups for phylogenomic estimation, including mayflies (Miller et al. 2018, Ogden et al. 2019). These methods have led to the largest and most robust analyses for Ephemeroptera to date. Still, the biggest obstacle posed by NGS and AHE is that it produces immense amounts of data that require processing before a phylogenetic data set can be finalized for analysis. We are interested in developing an improved workflow for processing these kinds of data. The workflow that has been developed will trim the raw reads, assemble the genome sequences, align the genome sequences for comparison, and assign orthology. Throughout the workflow, both taxa and loci with low representation in the data are filtered out to produce higher fidelity results. The overall analysis is expected to augment the number of taxa used in Ogden et al. (2019) and produce a more comprehensive phylogeny for the order. The workflow will be available on GitHub as part of the Ogden Lab after publication.