This README file was generated on 16-07-2021 by Cyril Hammoud. Data linked to the publicaiton: Hammoud, C., Mulero, S., Van Bocxlaer, B., Boissier, J., Verschuren, D., Albrecht, C., Huyse, T., Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing. (MER-20-0435) Additional data linked to this project are stored GenBank / NCBI SRA: PRJNA743924 List of files included, description and abbreviations: unique_ASVs_dada2.fasta : Fasta file containing all unique Amplicon Sequence Variants obtained from the HTAS workflow (before filtering based on read-support). Variables / acronyms: none infection.csv : Table with details on the parasite exposure and time of sacrifice for samples of the infection experiments. Variables / acronyms: -SampleID = Unique sample identifier -Timing = time of sacrifice, in days after exposure to parasite. -Infection: B = exposure to Schistosoma mansoni Bre; L = exposure to Schistosoma mansoni LE; R = exposure to Schistosoma rodhaini: BL = exposure to Schistosoma mansoni Bre + LE; RL = exposure to Schistosoma mansoni LE + Schistosoma rodhaini RD_diagnostic.csv : Table with the resutls of the Rapid Diagnostic-PCR assay for each sample. Variables / acronyms: -SampleID = Unique sample identifier -diagnostic_RD = result of the Rapid Diagnostic-PCR with: pos = positive signal; neg = negative signal; faint = faint signal (assimilated positive) seqtab_nochim_long.csv : Table summarizing the occurence of Amplicon Sequence Variants in each sample with read support. Variables / acronyms: -sample = sample ID from the sequencing facility -sequence = Amplicon Sequence Variant sequence -count = number of reads attributed to the specific Amplicon Sequence Variant -for the specific sample -shortID = ID containing only the PCR plate number and the well number, separated by "_" -sampleID = ID corresponding to the experimental conditions of the sample (see infection.csv) -prop = proportion of reads attributed to the specific Amplicon Sequence Variant for the specific sample (compared to the total read count of the sample) -seqID = unique ID of the Amplicon Sequence Variant -length_seq = number of nucleotides in the sequence -tot_reads = total number of reads for the sample BLAST_expected.csv : Basic Local Alignment Search Tool (BLAST) results expected for each sample. Variables / acronyms: -expected_BLAST_snail = BLAST result expected for snail Amplicon Sequence Variants. Lym = Lymneid; Bglab = Biomphalaria; Bul = Bulinus -expected_BLAST_dig1 = BLAST result expected for parasite Amplicon Sequence Variant in case of single infection or in co-infection. Srod = Schistosoma rodhaini; Sman = Schistosoma mansoni; Digsp = Digenea -expected_BLAST_dig2 = BLAST results expected for parasite Amplicon Sequence Variant in co-infection only. Srod = Schistosoma rodhaini; Sman = Schistosoma mansoni; Digsp = Digenea BLASTED.csv : Basic Local Alignment Search Tool (BLAST) results for the unique Amplicon Sequence Variants encountered, with information on the marker sequenced. Variables / acronyms: Lym = Lymneid; Bglab = Biomphalaria; Bul = Bulinus; Srod = Schistosoma rodhaini; Sman = Schistosoma mansoni; Digsp = Digenea primer_removal.txt : bash script to remove primers from raw reads using cutadapt. Variables / acronyms: N.A. dada2_script.R : R script to process raw reads of the core MiSeq v3 analysis into Amplicon Sequence Variants using dada2. Variables / acronyms: N.A. dada2_script_nano.R : R script to process raw reads of the preliminary Miseq nano v2 analyses into Amplicon Sequence Variants using dada2. Variables / acronyms: N.A amplicon_analysis.Rmd : R script to analyze the Amplicon Sequence Variants of each sample. Variables / acronyms: N.A. ASV_analysis_environment.RData : R environment for the amplicon_analysis.Rmd script. Variables / acronyms: N.A. COI1_snail_alignment.nex : Alignment of GenBank sequences used to design the primer for the COI1_snail marker. Contains accession IDs. Variables / acronyms: none COI1_trematode_alignment.nex : : Alignment of GenBank sequences used to design the primer for the COI1_trematode marker. Contains accession IDs. Variables / acronyms: none COI2_snails_alignment.nex : Alignment of GenBank sequences used to design the primer for the COI2_snail marker. Contains accession IDs. Variables / acronyms: none COI2_trematode_alignment.nex : Alignment of GenBank sequences used to design the primer for the COI2_trematode marker. Contains accession IDs. Variables / acronyms: none cytb_trematode_alignment.nex : Alignment of GenBank sequences used to design the primer for the cytb_trematode marker. Contains accession IDs. Variables / acronyms: none ITS1_snail_alignment.nex : Alignment of GenBank sequences used to design the primer for the ITS1_snail marker. Contains accession IDs. Variables / acronyms: none ITS2_trematode_alignment.nex : : Alignment of GenBank sequences used to design the primer for the ITS2_trematode marker. Contains accession IDs. Variables / acronyms: none NAD1_snails_alignment.nex : Alignment of GenBank sequences used to design the primer for the NAD1_snail marker. Contains accession IDs. Variables / acronyms: none NAD1_trematode_alignment.nex : Alignment of GenBank sequences used to design the primer for the NAD1_trematode marker. Contains accession IDs. Variables / acronyms: none For any inquiry please contact Cyril Hammoud: cyril.hammoud@ugent.be