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:
Installation¶
If you don’t have Python 3.4 or greater installed, be sure to get it. 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 a look at the User Guide.
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
@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}
}