title: COI amplicon seq of horse Strongylidae
design: Feces was collected from 48 naturally infected horse foals and mares from three commercially operated breeding farms in Germany during a longitudinal study in 2022. Strongyle-type eggs were extracted from positive faecal samples and DNA was isolated using the NucleoSpin Soil kit (Macherey-Nagel, Dren, Germany). The COI_Nema_Fw and COI_Nema_Rv primers (Duscher et al., 2015) with incorporated ILLUMINA adapter sequences were used in the first PCR. Indices were added in a second PCR using uniquie combinatios of P7 and P5 primers. The KAPA HiFi HotStart ReadyMix was used for all PCR amplifications. Final PCR products were purified using CleanNGS magnetic beads at a ratio of 10:8. DNA concentrations were quantified with a Qubit 4 fluorometer, and fragment quality was evaluated using the TapeStation system. All samples were sequenced on an Illumina MiSeq platform using the V3 600-cycle kit (2  300 bp). Following demultiplexing and quality filters, reads from both ends of each sample were paired using the justConcatenate mode of DADA2s mergePairs function. BLASTn (Altschul et al., 1990) was used to filter out ASVs that did not match at least  80% matching identity and  90% query coverage inside the Strongylidae family. The COI-database (Diekmann et al., 2025) was used to assign species.