Version Compatibility

Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

QIIME2 Amplicon Workflow

"Run my amplicon analysis through QIIME2" → Process 16S/ITS amplicon data end-to-end using the QIIME2 CLI with built-in provenance tracking, from import through denoising, taxonomy, and diversity analysis.

• CLI: qiime dada2 denoise-paired, qiime diversity core-metrics-phylogenetic

Import Data

# Import paired-end FASTQ with manifest
qiime tools import \
    --type 'SampleData[PairedEndSequencesWithQuality]' \
    --input-path manifest.tsv \
    --output-path demux.qza \
    --input-format PairedEndFastqManifestPhred33V2

# View demultiplexed summary
qiime demux summarize \
    --i-data demux.qza \
    --o-visualization demux.qzv

Denoise with DADA2

# DADA2 denoising (creates ASV table + representative sequences)
qiime dada2 denoise-paired \
    --i-demultiplexed-seqs demux.qza \
    --p-trunc-len-f 240 \
    --p-trunc-len-r 160 \
    --p-trim-left-f 0 \
    --p-trim-left-r 0 \
    --p-max-ee-f 2 \
    --p-max-ee-r 2 \
    --p-n-threads 0 \
    --o-table table.qza \
    --o-representative-sequences rep-seqs.qza \
    --o-denoising-stats denoising-stats.qza

# View denoising stats
qiime metadata tabulate \
    --m-input-file denoising-stats.qza \
    --o-visualization denoising-stats.qzv

Alternative: Deblur Denoising

# Quality filter first
qiime quality-filter q-score \
    --i-demux demux.qza \
    --o-filtered-sequences demux-filtered.qza \
    --o-filter-stats filter-stats.qza

# Deblur denoise
qiime deblur denoise-16S \
    --i-demultiplexed-seqs demux-filtered.qza \
    --p-trim-length 250 \
    --p-sample-stats \
    --o-representative-sequences rep-seqs-deblur.qza \
    --o-table table-deblur.qza \
    --o-stats deblur-stats.qza