Metagenomics inputs and parameters
FASTQ formats, database selection, diversity metrics, statistical methods, and configuration options for all metagenomics tools.
You provide raw FASTQ reads for classification and profiling, or a pre-computed abundance table (plus sample metadata) for diversity and differential-abundance analysis. Choosing the classifier and reference database that match your data — Kraken2/Centrifuge/Kaiju or MetaPhlAn/Bracken/mOTUs, WGS or 16S — is what most affects how many reads are assigned and how accurate the species calls are.
Metagenomics inputs and parameters
Common input formats
| Input | Format | Example | Accepted By |
|---|---|---|---|
| FASTQ reads (single-end) | .fastq, .fastq.gz | sample_R1.fastq.gz | metagenomics_classify, metagenomics_profile |
| FASTQ reads (paired-end) | Two .fastq.gz files | sample_R1.fastq.gz, sample_R2.fastq.gz | metagenomics_classify |
| Abundance table | URI (taxonomic abundance table produced by metagenomics_profile) | -- | microbiome_diversity, microbiome_differential |
| Sample metadata | CSV, sample/group or sample/condition columns | -- | microbiome_diversity, microbiome_differential |
Metagenomics Classify parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
fastq_uri | string | Yes | -- | URI of the FASTQ file (R1 or single-end) |
fastq_r2_uri | string | No | -- | URI of the R2 FASTQ file (paired-end) |
method | string | No | "kraken2" | Classification algorithm: "kraken2", "centrifuge", "kaiju" |
database | string | No | "standard" | Reference database: "standard", "silva", "greengenes" |
confidence | number | No | 0.1 | Minimum confidence score for classification |
Metagenomics Profile parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
fastq_uri | string | Yes | -- | URI of the FASTQ file |
method | string | No | "metaphlan" | Profiling method: "metaphlan", "bracken", "motu" |
resolution | string | No | "species" | Taxonomic resolution for reporting: "species", "genus", "family" |
metagenomics_profile doesn't take a separate reference-database or R2 parameter — resolution and method are the only tuning knobs.
Microbiome Diversity parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
abundance_table_uri | string | Yes | -- | URI of the taxonomic abundance table (from metagenomics_profile) |
metadata_file_uri | string | Yes | -- | URI of a sample metadata CSV (sample, group columns) |
metrics | string | No | "both" | Diversity metrics to compute: "alpha", "beta", "both" |
beta_method | string | No | "bray_curtis" | Beta diversity distance method: "bray_curtis", "unifrac", "jaccard" |
Alpha diversity is reported as Shannon, Simpson, Chao1, and observed-species counts (see outputs) — there's no parameter to select a subset of alpha metrics.
Microbiome Differential parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
abundance_table_uri | string | Yes | -- | URI of the taxonomic abundance table |
metadata_file_uri | string | Yes | -- | URI of a sample metadata CSV (sample, condition columns) |
contrast | string | Yes | -- | Contrast to test, e.g. "disease_vs_healthy" |
method | string | No | "ancombc" | Differential abundance method (compositional-data-aware): "ancombc", "aldex2", "maaslin2" |
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