maxemil / nothofagus-metabarcoding Goto Github PK

This is a collection of scripts used for the publication Ectomycorrhizal fungal communities in andean-patagonian Nothofagus forests.

The general workflow was as follows:

1. get data as fastq files, perform trimming and assembly (merging) of paired-end reads. Sequencing data has been deposited under BioProject ID PRJNA970541.
2. filter short (<150bp) reads and remove potential chimeras
3. get stats (very slow) for each step of the preprocessing pipeline sequence_stats.py
4. perform taxonomic annotation using the ITS refSeq (PRJNA177353) Database bash chimera_malt.sh
5. summarise taxonomic annotations on different labels for each replicate and combined per plot get_tax_level.py
6. make abundance plot based on the order level make_abundance_plot.py
7. run FunGuild for ecological annotation on the genus level run_FunGuild.py
8. calculate diversity indices resp. Hill numbers Diversity_indices.R
9. perform NMDS NMDS.R