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microscape-nf

Amplicon sequencing analysis pipeline — from raw reads to interactive visualization

microscape-nf 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

The pipeline uses two bioconda packages for all computation:

  • papa2 — DADA2 denoising (filter, dereplicate, denoise, merge, chimera removal, taxonomy)
  • microscape — Downstream analysis (QC filtering, ordination, networks, visualization)

An R alternative is available via --lang R, which uses Bioconductor's dada2 and microscapeR.

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 (microscape)
    │
    ├── ASSIGN_TAXONOMY (papa2, parallel per DB)
    ├── BUILD_PHYLOGENY (microscape + MAFFT)
    ├── RENORMALIZE (microscape)
    │
    ├── ORDINATE (microscape, t-SNE/PCA)
    ├── NETWORK (microscape, SparCC)
    └── EXPORT_VIZ (microscape, JSON → Svelte)
Package Language Channel Purpose
papa2 Python bioconda DADA2 denoising
microscape Python bioconda Downstream analysis
microscapeR R Bioconductor R companion
microscape-nf Nextflow GitHub This pipeline