16S rRNA gene targeted-amplicon data processing including quality control, clustering, classification (using mothur)
Input: paired end sequence data
Jupyter notebook:
- imid_reanalysis_gh.ipynb
Scripts:
- sbatch_make_contigs.sh
- make_contigs.sh
- merge_fasta.sh
- groups_20dec2017.sh
- analysis_20dec2017.sh
- summary.single.sh
Inputs: An OTU count table obtained from above processing with taxanomic information for the OTUs and sample information (e.g. meta-data).
Scripts:
- microbiome_1stStep.r: data wrangling
- microbiome_2ndStep.r: data filtering, normalization and machine learning classification
- ***_batch.r files: sourced in the previous two files to do analyses in batch