Pipelines for analysing fungal diversity data
The repository is structured as followed:
- PROFUNGIS : Pipeline for processing raw Fungal ITS Sequences markers obtained from SRA to unique ZOTUs sequences.
- PROFUNGIS_post_processing : incorporation of new ZOTUs sequences into MDDB reference table "ref_sequence" and update of mapping table ZOTU reference SRA
- ncbi_data_aquistion : automatic pipeline for retrieving sequence read archive metadata that is associated to open source publication linked to metabarcoding studies.
please read the README files for each pipeline for running the relevant pipelines.