CITATION.cff

cff-version: 1.2.0
message: >-
  If you use this software, please cite it as below.
  A. De Souza Novaes and D. Jansen contributed equally (shared first authorship).
  A.M. Rezende and K. Vercauteren contributed equally (shared senior authorship).
type: software
authors:
  - family-names: De Souza Novaes
    given-names: Ane
    orcid: https://orcid.org/0000-0003-3089-2102
  - family-names: Jansen
    given-names: Daan
    orcid: https://orcid.org/0000-0003-4612-6891
  - family-names: de Block
    given-names: Tessa
    orcid: https://orcid.org/0000-0003-3294-0147
  - family-names: Coppens
    given-names: Sandra
    orcid: https://orcid.org/0009-0004-0812-0995
  - family-names: Ariën
    given-names: Kevin K.
    orcid: https://orcid.org/0000-0002-1340-4165
  - family-names: Selhorst
    given-names: Philippe
    orcid: https://orcid.org/0000-0002-4488-5790
  - family-names: Rezende
    given-names: Antonio Mauro
    orcid: https://orcid.org/0000-0003-4775-1779
  - family-names: Vercauteren
    given-names: Koen
    orcid: https://orcid.org/0000-0003-1472-9938
doi: "10.5281/zenodo.20430617"
title: "Metatropics: Human viral pathogen identification and consensus genome calling from nanopore metagenomic sequencing data."
abstract: >-
  Metatropics is a Nextflow pipeline for Oxford Nanopore metagenomic reads, focused on detecting human viral pathogens
  and creating viral consensus genomes. Workflows start from raw POD5 (with optional GPU basecalling) or pre-basecalled
  FASTQ, then proceed with read quality control, alignment, host depletion, and taxonomic profiling, followed by
  consensus genome building—polishing, refinement, and consensus calling. One container image per process keeps
  runs portable and reproducible under Docker, Singularity/Apptainer, and typical HPC setups.
version: 0.1.2
date-released: 2026-03-31
url: https://github.com/Clinical-Virology-Unit/Metatropics
license: MIT