Scripts for pairwise nucleotide identity graphs

Design of the nemabiome assay and selection of target genes<br>Publicly available known rDNA regions were assessed for their suitability to detect nematode clades containing key parasitic genera known to infect canines, humans and other animals. A curated database of relevant parasitic GIN rDNA regions was downloaded from NCBI’s GenBank (29.01.24) and aligned using MAFFT (Katoh &amp; Standley, 2013) to be able to assess the interspecific nucleotide diversity of different rDNA regions for the parasitic nematode clades, I, III, IV and V (Smythe et al., 2019). To compare nucleotide identity between rDNA loci of GIN clades, sequence alignments were firstly separated into 18S and ITS1-to-ITS2 regions for each clade and then dereplicated so that only one sequence from each GIN species was represented. For each locus, gaps in alignments were removed using trimAL (Capella-Gutiérrez et al., 2009) with the parameters -resoverlap 0.5 and -seqoverlap 50. Next, a pairwise nucleotide distance matrix was built using a custom python script is available in this folder entitled 'distance'. Finally, for each distance matrix, pairwise and median nucleotide identities were displayed using violin and jitter plots in R studio (R Core Team, 2021) with the packages ggplot2 (Wickham, 2011), and dplyr (Yarberry, 2021). See 'Nemabiome_rDNA_combined_script' within this folder for how this was achieved.<br>