These how-to guides each focus on a single analytical goal and show you the minimal set of actions needed to achieve it, regardless of where you are in a larger pipeline. They complement the tutorials, which follow complete dataset-driven analyses from start to finish.
Use these guides when you want to:
understand which MOSHPIT actions are involved in a specific task
find the right starting point for your data type
combine individual subworkflows into a custom pipeline
For help setting up the MOSHPIT suite, configuring parallelization, fetching data from SRA, or importing and exporting artifacts, see the Using MOSHPIT guides.
“I want to…” quick reference¶
| Goal | Starting data | Guide | Full tutorial |
|---|---|---|---|
| Assemble contigs from reads | Raw reads | How to assemble contigs | End-to-end tutorial, Cocoa tutorial |
| Bin contigs into MAGs | Contigs + reads | How to bin MAGs | End-to-end tutorial, Cocoa tutorial |
| Quality-control data at every stage | Reads / contigs / MAGs | Quality control at every step | Cocoa filtering |
| Get an early taxonomic overview | Reads or contigs | Early taxonomic composition | End-to-end taxonomy |
| Dereplicate MAGs and estimate abundance | Filtered MAGs + reads | Dereplicate MAGs and estimate abundance | End-to-end dereplication, Abundance estimation |
| Profile functional potential | Reads or dereplicated MAGs | How to profile functional potential | End-to-end functional profiling, Cocoa functional annotation |
Choosing a starting point¶
I have… | Next step | Relevant guides |
|---|---|---|
SRA accession IDs | Fetch reads with | Then: Quality control → Assemble contigs |
Raw FASTQ reads | Quality-filter with | |
Assembled contigs | Bin into MAGs or classify directly | |
MAGs | Dereplicate, estimate abundance, annotate | See the End-to-end tutorial for a complete worked example |
When to use these guides vs a tutorial¶
The tutorials (End-to-end MAG reconstruction, Cocoa fermentation) walk you through a complete analysis on a specific dataset—they are the best place to start if you are new to MOSHPIT. Each tutorial chapter builds on the previous one and explains the reasoning behind every step.
These how-to guides assume you already have some familiarity with MOSHPIT. They are concise recipes organized by goal rather than by dataset, making them useful as a reference once you are building your own pipelines.
How to read a guide¶
Each guide is structured as follows:
Goal — the QIIME 2 artifacts and visualizations you will produce
Prerequisites — what you need to have before you start
Action sequence — the minimal set of
moshcommands, with parsl parallelization as an optional tabQC checkpoint — what to inspect before moving to the next stage
Further reading — links to the corresponding tutorial chapter and autogenerated reference pages
Commands in these guides pass artifacts through a QIIME 2 cache (cache:key) rather than as standalone .qza files. Visualization outputs remain .qzv files so you can open them in QIIME 2 View. For more on caches, see How to use the QIIME 2 artifact cache.