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Squiggle specifications


Unique identifier OMICS_31944
Name Squiggle
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some raw DNA sequences.
Input format FASTA
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.3.1
Stability Stable
Maintained Yes




No version available


  • person_outline Benjamin Lee

Publication for Squiggle

Squiggle citations


ERP evidence for consumer evaluation of copycat brands

PLoS One
PMCID: 5842871
PMID: 29466469
DOI: 10.1371/journal.pone.0191475

[…] less confident []. LPC enhancement has also been reported for familiar compared with unfamiliar stimuli []. In a study by Voss and Paller (2008), when participants were asked to recognize a repeated squiggle as either meaningful or meaningless, LPC potentials were found to be associated with familiarity ratings during recognition irrespective of the level of meaningfulness []. In this study, we h […]


State of the art of robotic surgery related to vision: brain and eye applications of newly available devices

PMCID: 5798758
PMID: 29440943
DOI: 10.2147/EB.S148644

[…] m comprises the handheld manipulator, an optical tracking system, and a real-time controller. The manipulator incorporates a miniature Gough-Stewart platform actuated by six ultrasonic linear motors (SQUIGGLE® SQL-RV-1.8; New Scale Technologies, Inc., Victor, NY, USA). The custom-built optical tracking system (“Apparatus to Sense Accuracy of Position” or “ASAP”) provides the position and orientati […]


Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire

BMC Genomics
PMCID: 5530509
PMID: 28747151
DOI: 10.1186/s12864-017-3936-7

[…] ad to rejection of the DNA molecules, leading to the concept for ONT sequencing termed ‘Read Until’ described in [] which makes use of these two features for selective sequencing - briefly: real-time squiggle data is continuously compared to a user provided reference containing simulated squiggle data leading to ejection of the DNA strand from the pore by reversing the voltage []. To date this has […]


Promoting Pluralism in Counselling: an Untapped Source of Relational Mapping as Therapeutic Process

PMCID: 5674124
PMID: 29167586
DOI: 10.1007/s10447-017-9298-7

[…] orth (throwing the bobbin reel) and returning it safely back to himself could be seen as representing Ernst’s playful experimentation with growth.Along similar lines, Winnicott (), in his use of the ‘Squiggle’ drawing (a simple ‘squiggly’ line drawn on paper that can serve as a catalyst for a child’s creative expression), showed how he entered the emotional minds of children to open up new ways of […]


Sequencing and phasing cancer mutations in lung cancers using a long read portable sequencer

PMCID: 5726485
PMID: 29117310
DOI: 10.1093/dnares/dsx027

[…] so see ). To further refine the detected SNVs, we only considered the reads with no mismatches in the ±3 bp region. This filter was useful, likely reflecting the base call scheme of MinION, based on ‘squiggle,’ a five-base window.For the detected SNVs, we validated the correct identification rates by comparing these variants with the RNA-Seq data from Illumina HiSeq. The indicated precision and re […]


Advances in the Microbiome: Applications to Clostridium difficile Infection

PMCID: 5039486
PMID: 27657145
DOI: 10.3390/jcm5090083

[…] la epidemic in West Africa []. Furthermore, a recent study has developed a method to selectively sequence only specific regions of interest in DNA. The method termed “Read Until” uses a predetermined squiggle pattern from the sequence of DNA of interest as a reference and rejects non-matches, only sequencing regions that match the reference squiggle []. Further development and optimisation of this […]

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Squiggle institution(s)
Department of Computer Science, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Lab41, In-Q-Tel, Menlo Park, CA, USA

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