Repseqs (ASV Generation)

Generates ASVs using DADA2 (paired/single) or Deblur (single), with optional filtering and optional diversity visualizations; produces feature tables, representative sequences, and supporting summaries.

Key configuration

asv_method: dada2pe  # dada2pe | dada2se | deblur

# DADA2 examples
dada2_trunc_len_f: 0
dada2pe_trunc_len_r: 0
dada2_trim_left_f: 0
dada2pe_trim_left_r: 0

# Deblur examples
deblur_trim_length: 150
deblur_trim_left: 0

# Filtering (optional)
to_filter: false
repseq_min_length: 0
repseq_max_length: 100000
repseq_min_abundance: 0.0
repseq_min_prevalence: 0.0

Input sources:

  • From QA/QC: reuse the same run_name/output_dir or set qaqc_run_name to point at another QA/QC run.
  • External demultiplexed reads: provide fastq_qza_file (QIIME 2 artifact).
  • Metadata: set sample_metadata_file to a TSV/CSV (auto-generated if omitted).

Optional diversity outputs (alpha rarefaction + core metrics) require

plot_diversity: true
alpha_max_depth: 500
core_sampling_depth: 500

Outputs

  • [run_name]-table.qza, [run_name]-repseqs.qza
  • Stats/visualizations under stats/ including denoising summaries, feature-table summaries, sequence-length reports, and diversity plots (if enabled)

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