Scripts and data for the study: Descriptive trnL metabarcoding of plant items consumed by the edible orthopterans Gryllus bimaculatus and Locusta migratoria

This repository contains The pipeline for treating raw sequences, from demultiplexing to the taxonomic assignment with BLAST: script_SeqAnalysis_clean.bash The script to curate the trnL reference database using CRABS: trnL_DB_script.bash The curated trnL reference database used for taxonomic assignment: crabs_ncbi_nsdpy_insilico_aligned_uniq_filtered.fasta The R script used for the last data cleaning steps and to perform the visualisations in the study: Analysis.R The reposirtoy also contains the necessary input data (IL2_obiclean_uniq_sort_fulldb.tab) for the R script Analysis.R to perform the main analyses and figures of the study. The refinement of taxonomic assignements with the LCA algorithm in MEGAN is described in the manuscript and is also the input to the R script "IL2_blastout_blastn_final_dust-ex_taxpath.txt". The R script uses a custom R script "RRA_thresholding.R" to perform the empirical selection of the RRA threshold. It outputs a figure showing the cummulative number of taxa removed at each selected threshold and a table with the list of taxa removed by each threshold.