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https://github.com/IQTLabs/squiggle

📈 DNA Sequence Visualization for Humans
https://github.com/IQTLabs/squiggle

dna visualization

Last synced: 3 months ago
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📈 DNA Sequence Visualization for Humans

Host: GitHub
URL: https://github.com/IQTLabs/squiggle
Owner: IQTLabs
License: mit
Archived: true
Created: 2018-07-04T03:47:58.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2021-07-10T06:38:33.000Z (over 3 years ago)
Last Synced: 2024-07-28T21:52:59.525Z (3 months ago)
Topics: dna, visualization
Language: Python
Homepage: https://squiggle.readthedocs.io
Size: 4.21 MB
Stars: 39
Watchers: 6
Forks: 9
Open Issues: 7
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

Awesome-Bioinformatics - Squiggle - Easy-to-use DNA sequence visualization tool that turns FASTA files into browser-based visualizations. [ [paper-2018](https://pubmed.ncbi.nlm.nih.gov/30247632) | [web](https://squiggle.readthedocs.io/en/latest/) ] (Visualization / Genome Browsers / Gene Diagrams)

README

        # This repository has moved to https://github.com/Benjamin-Lee/squiggle







[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbty807-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/bty807)

[![Build Status](https://travis-ci.org/Lab41/squiggle.svg?branch=master)](https://travis-ci.org/Lab41/squiggle)

[![Docs](http://readthedocs.org/projects/squiggle/badge/?version=latest)](http://squiggle.readthedocs.io/en/latest/?badge=latest)

[![PyPI](https://img.shields.io/pypi/v/squiggle.svg)](https://pypi.org/project/squiggle/)

Squiggle is a two-dimensional DNA sequence visualization library that can turn FASTA sequence files like this:

    >lcl|NC_000011.10_cds_NP_000509.1_1 [gene=HBB]

    ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAG

    TTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGG

    GGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGT

    GCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACT

    GTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCA

    TCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAAT

    GCCCTGGCCCACAAGTATCACTAA

    >lcl|NC_005100.4_cds_NP_150237.1_1 [gene=HBB]

    ATGGTGCACCTGACTGATGCTGAGAAGGCTGCTGTTAATGGCCTGTGGGGAAAGGTGAACCCTGATGATG

    TTGGTGGCGAGGCCCTGGGCAGGCTGCTGGTTGTCTACCCTTGGACCCAGAGGTACTTTGATAGCTTTGG

    GGACCTGTCCTCTGCCTCTGCTATCATGGGTAACCCTAAGGTGAAGGCCCATGGCAAGAAGGTGATAAAC

    GCCTTCAATGATGGCCTGAAACACTTGGACAACCTCAAGGGCACCTTTGCTCATCTGAGTGAACTCCACT

    GTGACAAGCTGCATGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACATGATTGTGATTGTGTTGGGCCA

    CCACCTGGGCAAGGAATTCTCCCCCTGTGCACAGGCTGCCTTCCAGAAGGTGGTGGCTGGAGTGGCCAGT

    GCCCTGGCTCACAAGTACCACTAA

into gorgeous, interactive visualizations like this:



    

    



(Click the picture to view an [interactive version](https://htmlpreview.github.io/?https://github.com/Lab41/squiggle/blob/master/docs/figures/hbb_comparison.html).)

## Installation

If you don't have Python 3.5 or greater installed, be sure to [get it](https://www.python.org/downloads/).

To get the current stable version of Squiggle, run:

    $ pip install squiggle

Or, alternatively, if you want to get the latest development version:

    $ pip install git+https://github.com/Lab41/squiggle.git

## Usage

Using Squiggle is as easy as:

    $ squiggle your_sequence.fasta

Squiggle has tons of options available to make beautiful, interactive visualizations of DNA sequences.

To get a full rundown of the various option, take look at the documentation [here](https://squiggle.readthedocs.io).

## Citation

Using Squiggle in your research? Please cite it!

- Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. _Bioinformatics_. doi:[10.1093/bioinformatics/bty807](doi.org/10.1093/bioinformatics/bty807)

```

@article{Lee2018,

  doi = {10.1093/bioinformatics/bty807},

  url = {https://doi.org/10.1093/bioinformatics/bty807},

  year  = {2018},

  month = {sep},

  publisher = {Oxford University Press ({OUP})},

  author = {Benjamin D Lee},

  editor = {John Hancock},

  title = {Squiggle: a user-friendly two-dimensional {DNA} sequence visualization tool},

  journal = {Bioinformatics}

}

```