waterway is an open source pipeline written in Bash and R that simplifies Qiime 2 microbiome analysis for 16S genomic data. The source code is available on GitHub here.
Features:
- Automatic execution of the Qiime2 workflow, based on a config file.
- Config file allows for easy and quick changes to variables used in Qiime2 commands.
- Steps that are completed are skipped on subsequent runs.
- Partially processed samples are not completely reprocessed, but are rather processed starting from the last completed step.
- Ex: Samples that have finished the DADA2 step skip all functions until the end of the DADA2 step, and instead start at tree generation.
- Smart exiting prompts users to enter information when needed.
- Can create classifier files for sk_learn based on the GreenGenes database, and can extract specific reads based on primer pairs.
- Easy, automatic creation of manifest files to use for importing data into Qiime2 if needed.
- Datasets can be subsetted to only include specific samples alongside the whole dataset.
- Multiple sub-datasets can be analysed automatically at the same time, depending on user needs.
- Support for multiple Qiime2 plugins, such as DEICODE and Picrust2.
- Support for data export to R via a phyloseq-formatted data dump that can be imported after analysis finishes.