H.J. Andrews Malaise-trap metabarcoding dataset, Session 1

These are the scripts to prepare the input data files for the eDNAPlus software (https://github.com/alexdiana1992/eDNAplus). Data file origin: We collected 121 Malaise-trap samples from 89 sample sites in and around the HJ Andrews Experimental Forest, Oregon. Each sample was subjected to the Begum metabarcoding pipeline (described in Yang, C.Y., Bohmann, K., Wang, X.Y., Wang, C., Wales, N., Ding, Z.L., Gopalakrishnan, S., Yu, D.W. (2021) Biodiversity Soup II: A bulk-sample metabarcoding pipeline emphasizing error reduction. Methods in Ecology and Evolution 12:1252-1264. doi: 10.1111/2041-210X.13602.). In short, each sample was DNA-extracted and then PCR-amplified for a 313 base-pair fragment of the COI DNA-barcode gene (using Leray-FolDegenRev primer pair, described in Yang et al. 2021). In the Begum pipeline, each sample is independently PCRd three times and then library prepped and sequenced on an Illumina sequencer (amplicon sequencing). Finally, we processed the Illumina output files to trim low-quality sequences, merge read pairs, and assign the orginating sample name to each read. Unlike in the standard Begum pipeline, we did not use the 3 separate PCRs per sample to detect and filter out erroneous sequences. Instead, we accepted all reads (i.e. by filtering at the no stringency: accepting reads if they appeared in ≥1 PCR with ≥1 read). This resulting fasta-format read dataset is the starting dataset for the custom scripts in this archive. This custom scripts generate 3 separate OTU tables (sample x species tables) from the 3 separate PCRs. The 3 OTU data tables are the raw inputs to eDNAPlus. The scripts and data files are also uploaded to datadryad.org as a single zip file