Overview¶
MetaFlux is a Snakemake workflow that takes raw
paired-end short reads through to a taxonomically annotated abundance table. It
covers two kinds of study — marker-gene metabarcoding and shotgun metagenomics — and a
single key in the config file, mode, decides which of the two runs. This site
documents version v2.3.0.
MetaFlux belongs to the BioFlux family of pipelines.
The two modes¶
amplicon |
shotgun |
|
|---|---|---|
| Input | PCR products from one marker gene | untargeted whole-genome sequencing reads |
| Core tools | DADA2 | Kraken2 + Bracken |
| Markers | 16S rRNA, ITS, 18S rRNA, gyrB, rpoB | not applicable |
| Main steps | PhiX removal, primer trimming, exact ASV inference, optional marker-region extraction, length filtering, taxonomy | decontamination, quality trimming, read classification, abundance re-estimation, OTU-table construction |
| Reference data | SILVA (16S), UNITE (ITS), PR2 (18S), DD7RZ8 (gyrB), FROGS (rpoB) — fetched automatically on first use | a Kraken2 database, supplied by the user |
| Final table | 6.taxonomy/asv_table.txt |
03.abundance/otu_table.tsv |
Amplicon mode resolves sequences exactly rather than clustering them at an arbitrary similarity threshold: DADA2 infers amplicon sequence variants (ASVs), which are then length-filtered and classified against the reference database that matches the marker. See the amplicon overview and the per-marker pages.
Shotgun mode skips amplification altogether and assigns whole-genome reads directly against a Kraken2 index, with Bracken re-estimating abundances at the chosen taxonomic level. See the shotgun overview.
One command, one config, one report¶
Both modes are launched the same way, from the repository root:
--sdm conda (short for --software-deployment-method) tells Snakemake to build each
rule's own conda environment on first run, so only Snakemake itself (version 9 or
newer) has to be installed by hand.
Everything else — mode, input and output paths, marker, primers, databases, per-rule CPU
and memory — lives in config/config.yaml. Both modes finish by writing read-tracking
statistics and a single MultiQC report under
multiqc/multiqc_report.html, so a run can be checked end to end from one HTML file.
What has to be prepared in advance
Amplicon runs need only the primer FASTAs: the marker reference databases download
themselves the first time they are needed and are cached under refdb/. Shotgun
runs need a Kraken2 database on disk before the first launch — these are large and
version-sensitive, so MetaFlux never fetches one automatically. See
Installation and
Reference databases.
Where to go next¶
| Page | Read it for |
|---|---|
| Installation | cloning the repository, the Snakemake launcher environment, reference databases |
| Quick start | the shortest path from a clone to a finished run |
| Choosing a mode | which mode a given dataset belongs in, and what happens if the wrong one is set |
| Amplicon mode | the DADA2 path step by step, marker by marker |
| Shotgun mode | the Kraken2 + Bracken path step by step |
| Configuration | every config key, what consumes it, and its default |
| Output files | what each output directory holds and which files are the deliverables |
| Running MetaFlux | dry runs, resuming, cluster execution |
| Troubleshooting | the failure modes that come up in practice, and how to get past them |
| Rationale | why the workflow makes the choices it does |
| Citation and references | how to cite MetaFlux and the tools it calls |
MetaFlux is released under the MIT License. The tools it invokes carry their own licenses.