{"id":13704251,"url":"https://github.com/IQTLabs/squiggle","last_synced_at":"2025-05-05T09:33:34.327Z","repository":{"id":56623000,"uuid":"139665471","full_name":"IQTLabs/squiggle","owner":"IQTLabs","description":"📈 DNA Sequence Visualization for 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Browsers / Gene Diagrams"],"readme":"# This repository has moved to https://github.com/Benjamin-Lee/squiggle\n\n\u003cp align =\"center\"\u003e\n\u003cimg src='https://github.com/Lab41/squiggle/raw/master/images/logo.png' height=\"150\"\u003e\n\u003c/p\u003e\n\n[![DOI](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbty807-brightgreen.svg)](https://doi.org/10.1093/bioinformatics/bty807)\n[![Build Status](https://travis-ci.org/Lab41/squiggle.svg?branch=master)](https://travis-ci.org/Lab41/squiggle)\n[![Docs](http://readthedocs.org/projects/squiggle/badge/?version=latest)](http://squiggle.readthedocs.io/en/latest/?badge=latest)\n[![PyPI](https://img.shields.io/pypi/v/squiggle.svg)](https://pypi.org/project/squiggle/)\n\nSquiggle is a two-dimensional DNA sequence visualization library that can turn FASTA sequence files like this:\n\n    \u003elcl|NC_000011.10_cds_NP_000509.1_1 [gene=HBB]\n    ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAG\n    TTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGG\n    GGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGT\n    GCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACT\n    GTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCA\n    TCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAAT\n    GCCCTGGCCCACAAGTATCACTAA\n    \u003elcl|NC_005100.4_cds_NP_150237.1_1 [gene=HBB]\n    ATGGTGCACCTGACTGATGCTGAGAAGGCTGCTGTTAATGGCCTGTGGGGAAAGGTGAACCCTGATGATG\n    TTGGTGGCGAGGCCCTGGGCAGGCTGCTGGTTGTCTACCCTTGGACCCAGAGGTACTTTGATAGCTTTGG\n    GGACCTGTCCTCTGCCTCTGCTATCATGGGTAACCCTAAGGTGAAGGCCCATGGCAAGAAGGTGATAAAC\n    GCCTTCAATGATGGCCTGAAACACTTGGACAACCTCAAGGGCACCTTTGCTCATCTGAGTGAACTCCACT\n    GTGACAAGCTGCATGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACATGATTGTGATTGTGTTGGGCCA\n    CCACCTGGGCAAGGAATTCTCCCCCTGTGCACAGGCTGCCTTCCAGAAGGTGGTGGCTGGAGTGGCCAGT\n    GCCCTGGCTCACAAGTACCACTAA\n\ninto gorgeous, interactive visualizations like this:\n\n\u003cp align =\"center\"\u003e\n    \u003ca href=\"https://htmlpreview.github.io/?https://github.com/Lab41/squiggle/blob/master/docs/figures/hbb_comparison.html\"\u003e\n    \u003cimg src=\"https://github.com/Lab41/squiggle/raw/master/images/HBB_squiggle.png\" alt=\"Human Squiggle\" width=\"750px\"/\u003e\n\u003c/p\u003e\n\n(Click the picture to view an [interactive version](https://htmlpreview.github.io/?https://github.com/Lab41/squiggle/blob/master/docs/figures/hbb_comparison.html).)\n\n## Installation\n\nIf you don't have Python 3.5 or greater installed, be sure to [get it](https://www.python.org/downloads/).\nTo get the current stable version of Squiggle, run:\n\n    $ pip install squiggle\n\nOr, alternatively, if you want to get the latest development version:\n\n    $ pip install git+https://github.com/Lab41/squiggle.git\n\n## Usage\n\nUsing Squiggle is as easy as:\n\n    $ squiggle your_sequence.fasta\n\nSquiggle has tons of options available to make beautiful, interactive visualizations of DNA sequences.\nTo get a full rundown of the various option, take look at the documentation [here](https://squiggle.readthedocs.io).\n\n## Citation\n\nUsing Squiggle in your research? Please cite it!\n\n- 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)\n\n```\n@article{Lee2018,\n  doi = {10.1093/bioinformatics/bty807},\n  url = {https://doi.org/10.1093/bioinformatics/bty807},\n  year  = {2018},\n  month = {sep},\n  publisher = {Oxford University Press ({OUP})},\n  author = {Benjamin D Lee},\n  editor = {John Hancock},\n  title = {Squiggle: a user-friendly two-dimensional {DNA} sequence visualization tool},\n  journal = {Bioinformatics}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FIQTLabs%2Fsquiggle","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FIQTLabs%2Fsquiggle","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FIQTLabs%2Fsquiggle/lists"}