clystere

clystere is a Nextflow pipeline for automated biosynthetic gene cluster (BGC) discovery and comparative analysis. It runs antiSMASH, GECCO, and deepBGC across a collection of bacterial or fungal genomes, merges overlapping predictions with comBGC, and optionally groups representative BGCs into gene cluster families (GCFs) with BiG-SCAPE or BiG-SLiCE.

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Overview

graph LR
    A[Genome assemblies<br/>samplesheet.csv] --> B[ANTISMASH<br/>per-genome]
    A --> C[GECCO<br/>per-genome]
    A --> D[deepBGC<br/>per-genome]
    B --> E[TABULATE_REGIONS<br/>all_regions.tsv]
    B --> F[COUNT_REGIONS<br/>region_counts.tsv]
    B --> G[comBGC unification]
    C --> G
    D --> G
    G --> H[BIGSCAPE dereplicate + cluster<br/>optional]
    G --> I[BIGSLICE cluster<br/>optional]

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Features

• Parallel antiSMASH + GECCO + deepBGC annotation across any number of genome assemblies or GenBank files
• comBGC-based unification of overlapping predictions before clustering
• Per-region tabulation and per-genome BGC count summary
• Optional BiG-SCAPE or BiG-SLiCE clustering (mutually exclusive)
• Optional BiG-SCAPE dereplication of redundant regions before clustering

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Quick start

nextflow run exterex/clystere \
    --input samplesheet.csv \
    --outdir results \
    -profile docker

See Installation and Usage for full details.