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danaSeq illumina_amplicon

Amplicon sequencing analysis pipeline — from raw reads to interactive visualization

danaSeq illumina_amplicon is a Nextflow DSL2 pipeline for amplicon sequencing analysis. It takes demultiplexed paired-end FASTQ files and produces ASV tables, multi-database taxonomy, phylogenies, ordinations, and correlation networks.

Architecture

Denoising is papa2 (a DADA2 port: filter, dereplicate, denoise, merge, chimera removal, taxonomy). Everything downstream — QC filtering, ordination, networks, visualization — is carried by this stage's own scripts in bin/.

Raw FASTQ files
    │
    ├── REMOVE_PRIMERS (cutadapt)
    ├── DADA2_FILTER_TRIM (papa2)
    ├── DADA2_LEARN_ERRORS (papa2, per-plate)
    ├── DADA2_DENOISE (papa2, per-plate)
    ├── MERGE_SEQTABS
    ├── REMOVE_CHIMERAS (papa2)
    ├── FILTER_SEQTAB (bin/)
    │
    ├── ASSIGN_TAXONOMY (papa2, parallel per DB)
    ├── BUILD_PHYLOGENY (bin/ + MAFFT)
    ├── RENORMALIZE (bin/)
    │
    ├── ORDINATE (bin/, t-SNE/PCA)
    ├── NETWORK (bin/, SparCC)
    └── EXPORT_VIZ (bin/, JSON → Svelte)
Project Purpose
papa2 DADA2 denoising (bioconda)
danaSeq This pipeline's home, alongside the metagenomics stages
microscape.app Hosting and sharing the interactive viz

The microscape (Python) and microscapeR (R) packages are retired. They mirrored this pipeline's downstream steps in two more places, which is how the truncation logic came to disagree with itself; that code now lives here in bin/, and the archived packages are reference snapshots only.