Sybr is a powerful bioinformatics tool meticulously designed for the discovery of synteny blocks, the precise identification of evolutionary breakpoints, and robust ancestral genome reconstruction. It serves as an essential resource for researchers in comparative genomics and evolutionary biology, enabling deeper insights into genomic architecture and evolutionary relationships.
- Synteny Block Discovery: Efficient algorithms to identify conserved genomic regions across multiple species.
- Evolutionary Breakpoint Identification: Pinpoint the precise locations where genomic rearrangements have occurred using the EBA module.
- Ancestral Genome Reconstruction: Algorithms to infer the genomic organization of common ancestors with DESCHRAMBLER.
- Enrichment Analysis: Perform functional enrichment on identified regions using getENRICH.
- Modular Workflow: Flexible
config.yamlto run specific stages of the analysis.
Example input files with pre-computed alignments:https://doi.org/10.6084/m9.figshare.32315682
Example input files without pre-computed alignments:https://doi.org/10.6084/m9.figshare.32315892
This project requires Conda to manage dependencies. If you already have Conda (Miniconda or Anaconda) installed, skip to this.
If Conda is not installed on your system, follow this step-by-step guide for Ubuntu:
Open a terminal and run:
conda --version- If you see something like
conda 24.x.x— Conda is already installed, skip the section below. - If you see
command not found— install Conda.
Clone the project from GitHub using the following command:
git clone https://github.com/your-username/sybr.gitGrant the necessary permissions to all files and directories:
chmod -R 777 SybrMove into the project folder:
cd SybrInstall all required dependencies by creating the Conda environment from the provided YML file:
conda env create -f install_sybr_dependence.ymlconda activate sybrThe link for sample data given above. To use this sample data, downloa this data. Sybr's workflow is controlled via a run_sybr_config.yaml file, allowing you to selectively run different analysis stages. User can check the Documentation for detailed understanding about config settings.
fast_track
├── Ancestor_seq_recunstruction
│ ├── LastZ_alignments
│ │ ├── sps2.axt
│ │ └── sps3.axt
│ ├── species_info.txt
│ └── tree.txt
├── eba_analysis
│ └── classification.eba
├── enrichment_analysis
│ └── protein_annotation.tsv
├── fasta
│ ├── Genus_sps1.fa
│ ├── Genus_sps2.fa
│ └── Genus_sps3.fa
└── synteny_processing
├── all_sequence_lengths.txt
└── Satsuma_alignments
├── Genus_sps2.txt
└── Genus_sps3.txt
Fixed filename — must use the exact name shown; the pipeline looks for it by name.
Variable — any filename is accepted; only the extension matters. Any number of files allowed.
Run LastZ with these recommended parameters for non-vertebrate species:
lastz reference.fa[multiple] query.fa \
C=0 E=30 H=2000 K=2200 L=2200 O=400 Y=3400 \
--format=axt --output=SpeciesName.axtUse the HoxD55 scoring matrix for distant/non-vertebrate comparisons.
The stem of each .axt filename (without extension) must match the names used in seq/, species_info.txt, and tree.txt.
Standard FASTA format. Accepts .fa, .fasta, .fna.
Both query and reference genomes must be present. The format of header should be >chr1, >chr2, >chr3, ... for chromosome level genome assembly and >scaf1, >scaf2, scaf3, ... for scaffold level genome assemply.
Three space/tab-separated fields per line, no header:
| Field | Values | Meaning |
|---|---|---|
| Species name | string | must match seq/, LastZ_alignments/, and tree.txt exactly |
| Role | 0 / 1 / 2 |
0 = reference · 1 = descendant · 2 = outgroup |
| Assembly level | 1 / 0 |
1 = chromosome-scale · 0 = scaffold-level |
Newick format, single line. Must start with ( and end with ;.
Two-column TSV: chromosome_name size_bp. Reference species only. Integer sizes.
Three-column TSV: sequence_name length_bp species. All sequences from all genomes.
Use the included genome_length_maker.sh script to generate this file.
Eight-column TSV output from Satsuma, no header:
query_chr q_start q_end ref_chr r_start r_end score strand
Strand must be + or -.
- In run_stages section, user can choose the pipeline modules to run. in frount of each module mane, type true for activate the module and false for deactivate the module.
- Use need to provide path for base_input_dir ( path of structured input folder) and base_output_dir (path of output folder).
- In reference_species provide the species name of referance only and in referance_name and r: provide genus and species name of referance.
- for r: in getenrich provide KEGG Organism code. user can check the availability of KEGG organims code in https://www.genome.jp/kegg/tables/br08606.html. if KEGG organism code is not availabe the user can use ko. for this option user need to provide kegg annotation file. to get the information about preparation of kegg annotation file refer to https://getenrich.igib.res.in/assets/files/getENRICH-documentation.pdf
# ─────────────────────────────────────────────────────────────────────────────
# run_sybr_config.yaml — User-facing config
# Edit this file to control pipeline behaviour
# ─────────────────────────────────────────────────────────────────────────────
# ── Base I/O directories ────────────────────────────────────────────────────
# Set these to absolute paths if your inputs/outputs live outside the
# workflow directory. Leave them as "inputs" / "outputs" to use the
# default folders relative to the workflow root.
base_input_dir: "/home/ajay.bhatia/Ajay_Bhatia/lab/Sybr-GUI7/mukul/inputs"
base_output_dir: "/home/ajay.bhatia/Ajay_Bhatia/lab/Sybr-GUI7/mukul/outputs"
# ── Pipeline stages to run ──────────────────────────────────────────────────
run_stages:
run_satsuma_alignment: false
run_lastz_alignment: false
synteny_processing: true
eba_analysis: false
enrichment_analysis: false
chainNet_generation: false
Ancestor_seq_recunstruction: false
# ── Species / reference names ───────────────────────────────────────────────
reference_name: "reference_sps"
reference_species: "sps"
# ── EBA parameters (user-facing) ───────────────────────────────────────────
eba:
n: 2 # number of EBA iterations
r: "Genus_sps1" # reference species name
p: 60 # resolution parameter # M
./sybr.sh -h
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============
========================================
Snakemake Pipeline
========================================
Usage: ./sybr.sh [OPTIONS]
Options:
-c, --config FILE Configuration file (default: run_sybr_config.yaml)
-P, --paths FILE Static paths file (default: pipeline_paths.yaml)
-j, --cores N Number of cores (default: all available)
-t, --target RULE Target rule (default: all)
-l, --log FILE Log output to file
-u, --unlock Unlock working directory
-n, --dry-run Dry run (simulate pipeline)
-k, --keep-going Keep going on independent job failures
-v, --verbose Verbose Snakemake output
-s, --skip-validation Skip input validation
-C, --clean Remove intermediate files after successful completion
-w, --window-sizes Comma-separated window sizes in bp (e.g., 100000,300000,500000)
-p, --step-size Step size in bp for synteny assignment (default: 30000)
-h, --help Show this help
Examples:
./sybr.sh -c config.yaml -j 8 # Run with default settings
./sybr.sh --window-sizes 200000,400000 --step-size 50000 # Custom window sizes and step size
./sybr.sh --window-sizes 100000 # Single window size
./sybr.sh --step-size 25000 # Custom step size with default windows
./sybr.sh --clean # Delete intermediate files after run
Note: Window sizes and step size only affect synteny_assign rules. If not specified,
defaults are: window sizes = 100000,300000,500000 and step size = 30000../sybr.sh -c run_sybr_config.yaml -j 8or
./sybr.sh -j 8or with clean -C flag
./sybr.sh -j 8 -C
./sybr.sh -w 200000,400000,500000 -j 8A comprehensive user manual and API documentation can be found in the docs/ directory or at [link_to_read_the_docs_if_applicable].
We welcome contributions to Sybr! If you'd like to contribute, please read our CONTRIBUTING.md for guidelines on how to submit pull requests, report issues, and suggest new features.
Encountered a bug or have a feature request? Please open an issue on our GitHub Issues page.
Sybr is released under the [LICENSE_NAME] License. See the LICENSE file for more details.
For questions or support, please contact [BioinformaticsOnLine@gmail.com] or open a discussion on GitHub.