---
title: Metagenomics inputs and parameters
description: >-
  FASTQ formats, database selection, diversity metrics, statistical methods, and
  configuration options for all metagenomics tools.
tags:
  - metagenomics
  - inputs
---

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](/docs/metagenomics/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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