Example data analyses

This section provides end-to-end examples for PipeCraft2 pre-compiled pipelines, showing what inputs to use, which key settings matter and what outputs to expect.

The examples are also a good way to learn the post-processing logic in PipeCraft2. Different pipelines (and marker types) may filter, curate, and summarize results in slightly different ways, so it is worth browsing multiple examples and comparing their post-processing steps and outputs.

• Inspect quality profiles
• DADA2 ASVs pipeline, 16S
• DADA2 ASVs pipeline, COI
• DADA2 ASVs pipeline, ITS2
• vsearch OTUs pipeline, ITS2
• OptimOTU pipeline, ITS2
• NextITS pipeline, full-length ITS
• FunBarONT pipeline, ITS