MetaManifold-WebUI/CITATION.cff at main · hyperpolymath/MetaManifold-WebUI · GitHub

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cff-version: 1.2.0
message: "If you use MetaManifold in academic work, please cite it as follows."
title: "MetaManifold: a Julia orchestrator for amplicon sequencing pipelines with an interactive web interface"
type: software
authors:
  - given-names: Joshua Benjamin
    family-names: Jewell
    email: jjewell23@rvc.ac.uk
    affiliation: "Royal Veterinary College"
    orcid: "https://orcid.org/0009-0007-0289-9741"
version: "0.1.0"
date-released: "2026-05-21"
license: AGPL-3.0-only
repository-code: "https://github.com/JoshuaJewell/MetaManifold-WebUI"
url: "https://github.com/JoshuaJewell/MetaManifold-WebUI"
abstract: >-
  MetaManifold is a Julia-native orchestrator for amplicon sequencing
  workflows. It wraps cutadapt, DADA2, SWARM, vsearch, and cd-hit-est into a
  single configurable pipeline, storing per-run results in DuckDB and exposing
  them through an interactive React frontend. Analyses include alpha diversity,
  taxonomic composition, NMDS, and PERMANOVA via R/vegan, together with
  cross-run comparison and a functional-database annotation layer.
keywords:
  - amplicon sequencing
  - metabarcoding
  - DADA2
  - SWARM
  - bioinformatics
  - Julia
  - DuckDB
references:
  - type: article
    title: "DADA2: High-resolution sample inference from Illumina amplicon data"
    authors:
      - family-names: Callahan
        given-names: "Benjamin J."
      - family-names: McMurdie
        given-names: "Paul J."
      - family-names: Rosen
        given-names: "Michael J."
      - family-names: Han
        given-names: "Andrew W."
      - family-names: Johnson
        given-names: "Amy Jo A."
      - family-names: Holmes
        given-names: "Susan P."
    journal: "Nature Methods"
    year: 2016
    volume: 13
    issue: 7
    start: 581
    end: 583
    doi: "10.1038/nmeth.3869"
  - type: article
    title: "Swarm v2: highly-scalable and high-resolution amplicon clustering"
    authors:
      - family-names: Mahe
        given-names: "Frederic"
      - family-names: Rognes
        given-names: "Torbjorn"
      - family-names: Quince
        given-names: "Christopher"
      - family-names: "de Vargas"
        given-names: "Colomban"
      - family-names: Dunthorn
        given-names: "Micah"
    journal: "PeerJ"
    year: 2015
    volume: 3
    start: e1420
    doi: "10.7717/peerj.1420"
  - type: article
    title: "VSEARCH: a versatile open source tool for metagenomics"
    authors:
      - family-names: Rognes
        given-names: "Torbjorn"
      - family-names: Flouri
        given-names: "Tomas"
      - family-names: Nichols
        given-names: "Ben"
      - family-names: Quince
        given-names: "Christopher"
      - family-names: Mahe
        given-names: "Frederic"
    journal: "PeerJ"
    year: 2016
    volume: 4
    start: e2584
    doi: "10.7717/peerj.2584"