EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis
- 1University College London
Abstract
Gene family expansion and contraction analysis is a commonly used approach in evolutionary comparative genomics to identify lineage-specific evolutionary pressures on gene copy/family number. CAFE is one of the most popular tools to measure changes in gene family size, but requires a high level of bioinformatics expertise, manual parameter tuning and preprocessing. Here we present EXCON, an automated, Eco-Flow community-developed Nextflow pipeline that integrates NCBI genome download, annotation quality and format pre-processing, orthologous gene family identification (Orthofinder), ultrametric tree formatting, birth-death modelling (CAFE), and GO enrichment analysis (eggNOG-mapper/TopGO) into a single, portable workflow. EXCON accepts genome assemblies and annotations, supports local, HPC and cloud-based computing environments, and requires minimal user configuration. The pipeline auto-selects appropriate CAFE lambda and error models, and separates high variance orthogroups for separate treatment. Applied to a 24-species primate dataset spanning Catarrhini, Platyrrhini and Strepsirrhini, the pipeline identified 358 rapidly evolving gene families, including a DUX (double homeobox) gene showing repeated, independent copy-number turnover across multiple lineages, consistent with the known instability of the D4Z4 macrosatellite repeat it resides in. EXCON is freely available at https://github.com/Eco-Flow/excon.
Related
- nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis
- Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis
- SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets
- DNAharvester: a nextflow pipeline for analysing highly degraded DNA from ancient and historical specimens
- Streamline CNV - A Handy Nextflow Pipeline for Chromosomal Copy Number Variation Analysis
BibTeX
@misc{wyatt2026excon,
title = {{EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis}},
author = {C. D. R. Wyatt and F. Duarte and A. Cerqueira De Araujo and S. Murray and C. Oi and S. Sumner},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.25.754512},
url = {https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis
AU - C. D. R. Wyatt
AU - F. Duarte
AU - A. Cerqueira De Araujo
AU - S. Murray
AU - C. Oi
AU - S. Sumner
PY - 2026
DA - 2026/09/25
PB - bioRxiv
DO - 10.64898/2026.09.25.754512
UR - https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1
AB - Gene family expansion and contraction analysis is a commonly used approach in evolutionary comparative genomics to identify lineage-specific evolutionary pressures on gene copy/family number. CAFE is one of the most popular tools to measure changes in gene family size, but requires a high level of bioinformatics expertise, manual parameter tuning and preprocessing. Here we present EXCON, an automated, Eco-Flow community-developed Nextflow pipeline that integrates NCBI genome download, annotation quality and format pre-processing, orthologous gene family identification (Orthofinder), ultrametric tree formatting, birth-death modelling (CAFE), and GO enrichment analysis (eggNOG-mapper/TopGO) into a single, portable workflow. EXCON accepts genome assemblies and annotations, supports local, HPC and cloud-based computing environments, and requires minimal user configuration. The pipeline auto-selects appropriate CAFE lambda and error models, and separates high variance orthogroups for separate treatment. Applied to a 24-species primate dataset spanning Catarrhini, Platyrrhini and Strepsirrhini, the pipeline identified 358 rapidly evolving gene families, including a DUX (double homeobox) gene showing repeated, independent copy-number turnover across multiple lineages, consistent with the known instability of the D4Z4 macrosatellite repeat it resides in. EXCON is freely available at https://github.com/Eco-Flow/excon.
ER -