An Illumina metabarcoding pipeline for fungi

摘要: High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning analyzing fungal barcode (ITS rDNA) data generated as paired-end reads Illumina MiSeq sequencers. The presented includes specific steps fine-tuned ITS, that mostly missing from pipelines developed prokaryotes. It (1) employs state the art programs follows best practices in high-throughput metabarcoding; (2) consists modules scripts easily modifiable by user ensure maximum flexibility with regard needs project or future methodological developments; (3) is straightforward use, also classroom settings. We detailed descriptions revision techniques each step, thus giving control over treatment avoiding black-box approach. Employing this will improve speed up tedious error-prone process cleaning