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squiggle

📈 DNA Sequence Visualization for Humans

https://github.com/benjamin-lee/squiggle

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • â—‹
    CITATION.cff file
  • â—‹
    codemeta.json file
  • â—‹
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • â—‹
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • â—‹
    Institutional organization owner
  • â—‹
    JOSS paper metadata
  • â—‹
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

📈 DNA Sequence Visualization for Humans

Basic Info
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Fork of IQTLabs/squiggle
Created about 5 years ago · Last pushed over 5 years ago

https://github.com/Benjamin-Lee/squiggle/blob/master/ 






[![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:



    
    Human Squiggle



(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}
}
```

Owner

  • Name: Benjamin Lee
  • Login: Benjamin-Lee
  • Kind: user
  • Location: Tysons, VA

NIH-OxCam scholar at @ncbi & DPhil student at Oxford. Previously @Harvard CS '20 and @IQTLabs

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 183
  • Total Committers: 3
  • Avg Commits per committer: 61.0
  • Development Distribution Score (DDS): 0.027
Top Committers
Name Email Commits
Benjamin Lee b****e@m****m 178
Matt Shirley m****5@g****m 4
Benjamin Lee b****e@c****u 1
Committer Domains (Top 20 + Academic)
college.harvard.edu: 1 me.com: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
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Issue Authors
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 96 last-month
  • Total docker downloads: 317
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 5
  • Total maintainers: 1
pypi.org: squiggle

DNA Sequence Visualization for Humans.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 96 Last month
  • Docker Downloads: 317
Rankings
Docker downloads count: 2.4%
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Average: 15.7%
Downloads: 21.2%
Stargazers count: 21.5%
Forks count: 29.8%
Maintainers (1)
Benjamin-Lee
Last synced: 11 months ago