Building a Reproducible Nextflow Pipeline for Metagenomics
Nextflow
Metagenomics
HPC
A minimal, worked example of structuring a metagenomics workflow in Nextflow so it is portable and reproducible.
Jul 24, 2026
Home
Bioinformatics scientist developing reproducible computational methods for microbiome, virome, and biomedical research.
Ricardo R. Pavan
Bioinformatics Scientist | Microbiome, Viromics & Reproducible Data Science
I develop reproducible bioinformatics pipelines and statistical/machine learning methods for microbiome, virome, and biomedical data — from raw sequencing reads to publication-ready results.
GitHub · LinkedIn · Google Scholar · ORCID · Email
What I do
Microbiome & Viromics
I design and run analyses that turn raw sequencing reads — 16S amplicon, shotgun metagenomic, and viral metagenomic data — into reliable, interpretable pictures of microbial and viral community structure, dynamics, and host interactions.
Bioinformatics Software & Pipelines
I build and maintain open-source tools (e.g. CRESSENT) and workflow pipelines that make specialized analyses reusable, tested, documented, and installable by other researchers — not one-off scripts.
Statistical Analysis & Machine Learning
I apply multivariate statistics, regression, classification, dimensionality reduction, and clustering to high-dimensional biological and environmental data, with attention to study design and validation, not just model fitting.
Reproducible Pipelines & HPC
I implement workflows in Nextflow and Snakemake, containerized with Docker/Apptainer and run on Slurm-managed HPC and research cyberinfrastructure (CyVerse, ACCESS, Tapis), so analyses can be rerun and verified by others.
Featured projects
CRESSENT
Problem: ssDNA viruses (CRESS viruses) lack consistent, reproducible annotation tools. Role: Lead developer. Methods: Python/R, motif & recombination analysis, CLI packaging. Impact: Published open-source toolkit distributed via PyPI/Bioconda (Microbial Genomics).
Python R PyPI Bioconda CLI
VirION3
Problem: Short-read-only sequencing struggles to recover complete, accurate viral genomes. Role: Developer, pipeline design. Methods: Long-read (Nanopore/PacBio) + Illumina hybrid assembly, benchmarking. Impact: Extends the VirION/VirION2 line of methods for viral genome recovery.
Nanopore PacBio Illumina Nextflow
Project details · Repository: link pending
BATS Diel Virome
Problem: Viral population dynamics at sub-daily timescales are rarely resolved in marine systems. Role: Co-lead, statistical/bioinformatic analysis. Methods: Time-series viral metagenomics, host prediction, depth-stratified sampling. Impact: Published in PLOS Biology.
Metagenomics Time-series Host prediction
Pig Burn Wound Microbiome
Problem: Understanding microbial community succession in a wound-healing model. Role: Bioinformatics analysis (assembly, binning, taxonomy). Methods: Nextflow, metagenomic assembly, genome binning, CheckM2, GTDB-Tk. Impact: Ongoing — generalized methods description (no unpublished results shown).
Nextflow Slurm Apptainer Metagenomics
Spinal Cord Injury Microbiome & Virome
Problem: How microbiome, virome, and phage–host dynamics shift after spinal cord injury. Role: Bioinformatics/statistical analysis. Methods: Longitudinal microbiome/virome profiling, mobile-element detection. Impact: Ongoing — generalized methods description.
Longitudinal Microbiome Virome
Macquarie Harbour Microbial Ecology
Problem: How environmental gradients and aquaculture shape microbial communities in a stratified estuary. Role: PhD research — lead. Methods: 16S/18S sequencing, network analysis, machine learning, db-RDA/PERMANOVA. Impact: Multiple peer-reviewed publications (2021–2022).
R Machine Learning Ecological Statistics
Selected outputs
- Publication — Pavan, Sullivan & Tisza (2026). CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation. Microbial Genomics. DOI
- Publication — Carrillo et al. (2026). Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics. PLOS Biology. DOI
- Software — CRESSENT: open-source ssDNA virus annotation toolkit (PyPI, Bioconda).
- Talk — CRESSENT: A Toolkit to Enhance ssDNA Virus Annotation. Midwest Microbiome Symposium, Columbus, OH (2025).
Latest from the blog
No matching items
Let’s talk
I’m glad to hear from people exploring research collaborations, bioinformatics or data-science projects, scientific software, biomedical/microbiome data analysis, employment opportunities, or workshop/talk invitations.