ntSynt-viz

KO | EN

gitlite — search

#hacktoberfest #react #typescript #llm #go #rust #deep-learning #docker #nodejs #awesome #kubernetes #ios #mcp #open-source

(★ 64)

Multi-genome synteny block visualization tool

ntSynt-viz 최신버젼 다운로드

최종 버전 다운로드 (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

![GitHub Release](https://img.shields.io/github/v/release/BirolLab/ntsynt-viz?display_name=release)
[![Preprint](https://img.shields.io/badge/ntSynt--viz-Preprint-6f42c1)](https://www.biorxiv.org/content/10.1101/2025.01.15.633221v2)

![Logo](https://github.com/BirolLab/ntSynt-viz/blob/main/ntsynt-viz_logo_colors.png)

# ntSynt-viz: Visualizing multi-genome synteny

1. [Credit](#credit)
2. [Description](#description)
3. [Dependencies](#dependencies)
4. [Installation](#install)
5. [Usage](#usage)
6. [Examples](#example)
7. [Interactive plots](#interactive-plots)
8. [Citing](#citing)
9. [License](#license)

## Credit  <a name=credit></a>
Written by Lauren Coombe

## Description <a name=description></a>
ntSynt-viz is an easy-to-use framework for generating static and interactive ribbon plots combined with chromosome painting to visualize multi-genome synteny blocks. The tool is set-up to accept synteny blocks formatted in the [ntSynt](https://github.com/BirolLab/ntSynt) style, but any multi-genome synteny block file that adheres to the simple, BED-like TSV format of ntSynt can be visualized using ntSynt-viz.

This flexible framework implements numerous features, including:
* Option to normalize the strands of input chromosomes based on a target assembly
* Synteny-guided ordering of assemblies from top-to-bottom, based on an input tree structure or distance estimates from the synteny blocks
* Sorting chromosomes right-to-left based on synteny to adjacent assemblies
* Colouring both the ribbons and chromosomes based on the target (top) assembly chromosomes
* Static and interactive ribbon plot outputs

These features ensure that the output ribbon plots (powered by [gggenomes](https://thackl.github.io/gggenomes/)) are as easily understandable and as information-rich as possible.

## Dependencies <a name=dependencies></a>
* python 3.8+
* [intervaltree](https://github.com/chaimleib/intervaltree)
* [snakemake](https://github.com/snakemake/snakemake)
* [quicktree](https://github.com/khowe/quicktree)
* [biopython](https://biopython.org/)
* R packages:
  * [gggenomes >=1.1.0](https://github.com/thackl/gggenomes)
  * [treeio](https://www.bioconductor.org/packages/release/bioc/html/treeio.html)
  * [ggpubr](https://rpkgs.datanovia.com/ggpubr/)
  * [ggtree](https://github.com/YuLab-SMU/ggtree)
  * [tidytree](https://cran.rstudio.com/web/packages/tidytree/index.html)
  * [phytools](https://cran.r-project.org/web/packages/phytools/index.html)
  * [dplyr](https://dplyr.tidyverse.org/)
  * [tidyr](https://tidyr.tidyverse.org/)
  * [argparse](https://cran.r-project.org/web/packages/argparse/index.html)
  * [scales](https://scales.r-lib.org/)
  * [stringr](https://stringr.tidyverse.org/)
  * [ggplot2](https://ggplot2.tidyverse.org)
  * [svglite](https://cran.r-project.org/web/packages/svglite/index.html)
  * [ggiraph](https://davidgohel.github.io/ggiraph/)

### Installing ntSynt-viz using conda <a name=install></a>
```
conda install -c conda-forge -c bioconda ntsynt-viz
```

### Running ntSynt-viz using the source code
Once all dependencies are installed, download the source code tarball, and add the `bin` directory to your PATH
```
wget https://github.com/BirolLab/ntSynt-viz/releases/download/v1.1.0/ntSynt-viz-1.1.0.tar.gz
tar xvzf ntSynt-viz-1.1.0.tar.gz
export PATH=/path/to/ntsynt-viz/github/ntSynt-viz/bin:$PATH
```

## Usage <a name=usage></a>
```
usage: ntsynt_viz.py [-h] --blocks BLOCKS --fais FAIS [FAIS ...] [--name_conversion NAME_CONVERSION] [--tree TREE] [--target-genome TARGET_GENOME] [--normalize]
                     [--indel INDEL] [--length LENGTH] [--seq_length SEQ_LENGTH] [--keep KEEP [KEEP ...]] [--centromeres CENTROMERES] [--haplotypes HAPLOTYPES]
                     [--order ORDER] [--prefix PREFIX] [--format {png,pdf,svg}] [--scale SCALE] [--height HEIGHT] [--width WIDTH] [--dpi DPI]
                     [--annotate-genome-info] [--optimize-ordering] [--no-arrow] [--ribbon_adjust RIBBON_ADJUST] [-f] [-n] [-v]

Visualizing multi-genome synteny

options:
  -h, --help            show this help message and exit

required arguments:
  --blocks BLOCKS       ntSynt-formatted synteny blocks TSV
  --fais FAIS [FAIS ...]
                        FAI files for all input genomes. Can be a list or a file with one FAI path per line.

main plot formatting arguments:
  --name_conversion NAME_CONVERSION
                        TSV for converting names in the blocks TSV (old -> new). IMPORTANT: new names cannot have spaces. If you want to have spaces in the
                        final ribbon plot, use the special character '_'. All underscores in the new name will be converted to spaces.
  --tree TREE           User-input tree file in newick format. If specified, this tree will be plotted next to the output ribbon plot, and used for ordering the
                        assemblies. The names in the newick file must match the new names if --name_conversion is specified, or the genome file names in the
                        synteny blocks input file otherwise. If not specified, the synteny blocks will be used to estimate pairwise distances for the genome
                        ordering and associated tree.
  --target-genome TARGET_GENOME
                        Target genome. If specified, this genome will be at the top of the ribbon plot, with ribbons coloured based on its chromosomes and (if
                        applicable) other chromosomes normalized to it. If not specified, the top genome will be arbitrary.
  --normalize           Normalize strand of chromosomes relative to the target (top) genome in the ribbon plots
  --centromeres CENTROMERES
                        TSV file with centromere positions. Must have the headers: bin_id,seq_id,start,end. bin_id must match the new names from
                        --name_conversion or the genome names if --name_conversion is not specified. seq_id is the chromosome name.
  --haplotypes HAPLOTYPES
                        File listing haplotype assembly names: TSV, maternal/paternal assembly file names separated by tabs.
  --order ORDER         Optional file specifying the order of genomes in the ribbon plot. If supplied, will override synteny distance-based ordering. If --tree
                        supplied, the ordering must be compatible with the phylogenetic tree.

block filtering arguments:
  --indel INDEL         Indel size threshold (used in computing synteny-based distances) [50000]
  --length LENGTH       Minimum synteny block length [100000]
  --seq_length SEQ_LENGTH
                        Minimum sequence length [500000]
  --keep KEEP [KEEP ...]
                        List of genome_name:chromosome to show in visualization. All chromosomes with links to the specified chromosomes will also be shown.

output arguments:
  --prefix PREFIX       Prefix for output files [ntSynt-viz_ribbon-plot]
  --format {png,pdf,svg}
                        Output format of plot [png]
  --scale SCALE         Length of scale bar in bases [100e6]
  --height HEIGHT       Height of plot in cm [20]
  --width WIDTH         Width of plot in cm [55]
  --dpi DPI             Resolution of output plot - png output only [300]
  --annotate-genome-info
                        Add annotations about number of sequences and genome size to the right of each genome in the ribbon plot
  --optimize-ordering   Optimize tree-guided genome sorting using inversions. Only use with strictly bifurcating trees.
  --no-arrow            Only used with --normalize; do not draw arrows indicating reverse-complementation
  --ribbon_adjust RIBBON_ADJUST
                        Ratio for adjusting spacing beside ribbon plot. Increase if ribbon plot labels are cut off, and decrease to reduce the white space to
                        the left of the ribbon plot [0.1]

execution arguments:
  -f, --force           Force a re-run of the entire pipeline
  -n                    Dry-run for snakemake pipeline
  -v, --version         show program's version number and exit
```
## Example commands <a name=example></a>
All the files referenced in these commands can be found in the `tests` subfolder for you to use in testing.

#### Plot ribbon plots with an input cladogram in newick format, normalizing the strands of the assembly chromosomes
```
ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv --tree great-apes.mt-tree.nwk --name_conversion great-apes.name-conversions.tsv --normalize --prefix great-apes_ribbon-plots --ribbon_adjust 0.14 --scale 1e9
```
![Example_ribbon_plot](https://github.com/BirolLab/ntSynt-viz/blob/main/tests/great-apes_ribbon-plots.example1.png)

#### Plot ribbon plots without input cladogram, skipping normalization of the assembly chromosome strands, specifying target (top) genome
```
ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv  --name_conversion great-apes.name-conversions.tsv  --prefix great-apes_ribbon-plots_no-tree --ribbon_adjust 0.15 --scale 1e9 --target-genome Homo_sapiens
```
![Example_ribbon_plot](https://github.com/BirolLab/ntSynt-viz/blob/main/tests/great-apes_ribbon-plots.example2.png)

For more information about the output files from ntSynt-viz, check out our [wiki page](https://github.com/BirolLab/ntSynt-viz/wiki).

## Using ntSynt-viz with pangenome graphs or synteny blocks from tools other than ntSynt
To visualize synteny information in pangenome graphs or from synteny block detection tools other than ntSynt, the synteny blocks simply need to be converted to the straightforward [ntSynt format](https://github.com/BirolLab/ntsynt?tab=readme-ov-file#output-files). For convenience, we also provide some scripts to do this conversion in the `conversion_scripts` directory.

## Interactive plots
As of v1.1.0, ntSynt-viz generates an HTML file to allow interactive exploration of the ribbon plot.

Interactive elements include:
* Hover/click on a ribbon to highlight the entire synteny block and display block coordinates and orientations
* Hover/click on a chromosome to display ID and length
* Click on one or more chromosomes in the legend to highlight the correseponding synteny blocks

Example interactive ribbon plot: https://www.birollab.ca/viz/ntsynt-viz.cheilosia_ribbon-plot_tree.html

## Using LLMs to summarize ribbon plots
As of v1.1.0, ntSynt-viz generates a markdown file (`*LLM-info.md`) that can be input to your LLM of choice (along with the PNG image output) to produce a brief summary of the ribbon plot.
Note that it is important to double check all conclusions/interpretations made by the LLM.

## Citing <a name=citing></a>

Thank you for your [![Stars](https://img.shields.io/github/stars/BirolLab/ntSynt-viz.svg)](https://github.com/BirolLab/ntSynt-viz/stargazers) and for using and promoting this free software! We hope that ntSynt-viz (& ntSynt) is useful to you and your research.

If you use nSynt-viz, please cite:

Coombe L, Kazemi P, Wong J, Birol I, Warren RL. 2025. ntSynt: multi-genome synteny detection using minimizer graph mappings. BMC Biology. 23:367. https://doi.org/10.1186/s12915-025-02455-w

and

[ntSynt-viz: Visualizing synteny patterns across multiple genomes](https://doi.org/10.1101/2025.01.15.633221)
<pre>
ntSynt-viz: Visualizing synteny patterns across multiple genomes
Lauren Coombe, Rene L Warren, Inanc Birol
bioRxiv 2025.01.15.633221; doi: https://doi.org/10.1101/2025.01.15.633221
</pre>

ntSynt-viz is released under the GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

For commercial licensing options, please contact Patrick Rebstein prebstein@bccancer.bc.ca

ntSynt-viz

ntSynt-viz 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

ntSynt-viz

ntSynt-viz 최신버젼 다운로드

오늘의 추천 프로젝트

Was this content helpful?

Recent Feedback

Download README