Software

Scientific software I develop and maintain.

CRESSENT

CRESSENT logo placeholder

Purpose: Modular toolkit for annotation and analysis of CRESS (circular Rep-encoding ssDNA) DNA viruses — motif detection, recombination analysis, stem-loop/iteron detection, sequence logos.

My role: Lead developer — design, implementation, testing, documentation, packaging, and manuscript.

Languages: Python, R

Status: Active — published and maintained

Documentation: GitHub repository

Repository: github.com/ricrocha82/cressent

Installation: PyPI and Bioconda (add exact install commands here once confirmed, e.g. pip install cressent / conda install -c bioconda cressent)

Citation: > Pavan, R.R., Sullivan, M.B. and Tisza, M., 2026. CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation. Microbial Genomics, 12:001632. https://doi.org/10.1099/mgen.0.001632

License: [PLACEHOLDER — confirm license, e.g. MIT/GPL-3.0]

Tests: Automated test suite (see repository)

Releases: See GitHub releases

Related publication: Microbial Genomics, 2026

flowchart LR
  A[CRESS virus genome] --> B[CRESSENT CLI]
  B --> C[Motif / structural annotation]
  B --> D[Recombination analysis]
  C --> E[Sequence logos + report]
  D --> E

VirION3

Purpose: Hybrid long- and short-read viromics workflow (Nanopore, PacBio, Illumina) for improved viral genome recovery.

My role: Developer, benchmarking analysis.

Languages: Nextflow, Bash, Python

Status: In development

Repository: link pending public release

Related project page: VirION3