Bioinformatic scripts allowing the comparison of fungal metabarcoding pipelines

This dataset contains scripts and code that can be used to compare metabarcoding pipelines using a fungal mock community. These bioinformatics scripts were applied to the sequences available at https://doi.org/10.15454/8CVWRR (Pauvert et al. Bioinformatics matters: the accuracy of plant and soil community data is highly dependent on the metabarcoding pipeline. Submitted). They can be used to compare the performance of 360 software and parameter combinations. They are based on several softwares, including USEARCH (Edgar 2010), VSEARCH (Rognes et al. 2016) and DADA2 (Callahan et al. 2016). The code corresponds mainly to bash scripts and R files. README files are provided for clarity.