D in this paper advantage the reader in additional pursuing individual amplicon sequencing at the same time as processing experiments.Abbreviations ABZ: Albendazole; ASVs: Amplicon sequence variants; FEC: Fecal egg count; GIN: Gastrointestinal nematode; ITS2: Internal transcribed spacer two; IVM: Ivermectin; MOP: Monepantel; NGS: Next-generation sequencing; OTUs: Operational taxonomic units.Supplementary InformationThe on-line version consists of supplementary material offered at doi. org/10.1186/s13071-022-05399-0. More file 1: Table S1. Sample names, anthelmintic drugs employed on farms where the samples were collected, the time at which the samples have been collected as well as the filtered, high-quality reads derived with all the DADA2, Mothur or SCATA pipelines, respectively. Note: Sample names in red correspond to samples (n=50) selected for the final evaluation on the effect with the pipeline(s) on the estimation of species abundance, richness and diversity. Extra file 2: Table S2. Mean relative frequencies of every nematode species in each pre- and post-treatment samples with the three analysis pipelines determined by the DADA2, SCATA or Mothur pipelines, respectively. Additional file 3: Figure S1. Alpha diversity (Inverse Simpson, 1/D) index comparisons in between the distinctive pipelines (DADA2, Mothur and SCATA) in both pre- (a) and post-treatment (b) sample categories. Acknowledgements We acknowledge DVM Katarina Gustafsson and Vidilab AB for their assist in collecting the samples applied in this study. We also acknowledge SLU Metabarcoding Laboratory-UMBLA for the PacBio library preparation and SciLifeLab in Uppsala, Sweden, for PacBio sequencing.Baltrusis et al. Parasites Vectors(2022) 15:Page 11 ofAuthor contributions The study was designed by JH and PH. PB analyzed the information and wrote the manuscript. Each JH and PH reviewed the manuscript and authorized it. Funding was acquired by JH. All authors read and authorized the final manuscript.ALDH4A1 Protein Formulation Funding Open access funding offered by Swedish University of Agricultural Sciences.GDF-15 Protein Formulation This perform was supported by the Swedish Foundation of Agricultural Research Grant O-16-20-742 and Formas 2016-1744.PMID:23746961 Availability of information and materials The ITS2 data used in this study is accessible upon request. The raw dataset has also been deposited to BioStudies (ebi.ac.uk/biostudies/) below the name S-BSST819.12.13.14. 15.DeclarationsEthics approval and consent to participate Parasites were collected from samples received for routine veterinary diagnostics. No ethical permission was thus expected. Consent for publication Not applicable. Competing interests The authors have no competing interests to declare. Received: 23 March 2022 Accepted: 13 July 2022 16. 17.18. 19.References 1. Charlier J, Rinaldi L, Musella V, Ploeger HW, Chartier C, Vineer HR, et al. Initial assessment of the economic burden of main parasitic helminth infections towards the ruminant livestock business in Europe. Prev Vet Med. 2020;182:105103. 2. Keegan JD, Superior B, de Waal T, Fanning J, Keane OM. Genetic basis of benzimidazole resistance in Teladorsagia circumcincta in Ireland. Ir Vet J. 2017;70:eight. 3. H lund J, Gustafsson K, Ljungstr BL, Skarin M, Varady M, Engstr F. Failure of ivermectin therapy in Haemonchus contortus infectedSwedish sheep flocks. Vet Parasitol Reg Stud Rep. 2015;1:10. 4. Rose Vineer H, Morgan ER, Hertzberg H, Bartley DJ, Bosco A, Charlier J, et al. Rising value of anthelmintic resistance in European livestock: creation and meta-analysis of an open information.