Kallisto alignment and gene annotation

For each species, Kallisto was used to perform ultra-fast read mapping of raw reads to a reference transcriptome (Bray et al. 2016). Quality controls for raw data and Kallisto alignments were assessed and summarized using FastQC v0.11.9 and MultiQC v1.9 (Andrews 2010; Ewels et al. 2016). Kallisto-generated transcript abundance data were imported into R v3.6.3 using the tximport package v1.14.2; transcript read counts were generated using the lengthScaledTPM option (Soneson et al. 2015).

Gene annotations were imported from WormBase ParaSite via the biomaRt package v2.42.1 (Durinck et al. 2005, 2009). Annotation information includes: C. elegans homologs/percent homology, UniProKB number, InterPro terms, gene ontology (GO) terms, and gene homologs/percent homology for the other three Strongyloides species.