SyBR

Multi-species synteny analysis and ancestral genome reconstruction pipeline

Automated pipeline for synteny analysis and ancestral genome reconstruction. Identifies conserved genomic blocks and evolutionary breakpoints across multiple species. Integrates EBA, DESCHRAMBLER, and getENRICH in a single modular workflow.

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Recent Updates

🔹 2026-04-28
SyBR Web Server Alpha
SyBR is now available as a hosted web service at sybr.igib.res.in. Submit jobs, track results, and download outputs directly from your browser — no local installation required.
🔹 2026-03-15
DESCHRAMBLER Integration
Added ancestral genome reconstruction support via DESCHRAMBLER. Infer ancestral genomic organization directly from LastZ alignments using a dedicated pipeline stage.
🔹 2026-02-10
Enrichment Analysis via getENRICH
Integrated the getENRICH module for functional enrichment of identified EBRs and msHSBs.

Explore the streamlined process

This workflow guides you from inputting your gene lists to obtaining comprehensive enrichment results and visualizations.

✨ Access CLI Documentation Sample Data

Modular Pipeline Workflow

Choose to run the entire pipeline end-to-end or execute individual modules based on your research needs.

Synteny Processing

Discover conserved genomic blocks across multiple species.

EBA Analysis

Identify evolutionary breakpoints with statistical confidence.

Enrichment Analysis

Perform KEGG pathway enrichment on regions of interest.

ChainNet Generation

Prepare hierarchical alignments for reconstruction.

Ancestral Reconstruction

Reconstruct the contiguous ancestral genome blocks.

Structured Data Inputs

SyBR uses a clear, structured directory format ensuring reproducibility and organized project management.

inputs/

Ancestor_seq_recunstruction/

└─ LastZ_alignments/, seq/, species_info.txt, tree.txt

eba_analysis/

└─ chr_size.txt, classification.eba, reference.fasta

enrichment_analysis/

└─ 3kegg_annotationTOgenes.txt, protein_annotation.tsv

synteny_processing/

└─ Satsuma_alignments/, all_sequence_lengths.txt

Simple Configuration.
Powerful Execution.

Control the entire SyBR workflow through a single, elegant YAML configuration file. Execute locally or on your HPC cluster with our optimized Snakemake wrapper.

Zero code required for basic usage
Granular control over specific modules
Scalable from laptops to compute clusters
Reproducible pipeline runs

# run_sybr_config.yaml
base_input_dir:  "/path/to/inputs"
base_output_dir: "/path/to/outputs"

run_stages:
  synteny_processing: true
  eba_analysis: true
  enrichment_analysis: true
  chainNet_generation: true
  Ancestor_seq_recunstruction: true

reference_name: "Adineta_vaga"
reference_species: "vaga"

eba:
  n: 5
  r: "Adineta_vaga"
  p: 300