PacmonSTR statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

Associated diseases

PacmonSTR specifications


Unique identifier OMICS_05208
Name PacmonSTR
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data An alignment file (alignment of long reads with the reference, such as, hg19) and a reference Tandem Repeat table.
Biological technology Pacific Biosciences
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
Computer skills Advanced
Stability Stable
Blasr, Cython, Scikit-learn
Maintained Yes



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  • person_outline Ali Bashir <>
  • person_outline Ajay Ummat <>

Publication for PacmonSTR

PacmonSTR in publication

PMCID: 5514472
PMID: 28720120
DOI: 10.1186/s13073-017-0456-7

[…] [], and trhist [], which screen for simple/intersperse repeats only for a query sequence. repeathmm is also different from lobstr [], which infers microsatellites from short-read sequencing data, or pacmonstr [], which needs detail alignment and repeat information of every long read and uses realignment to determine repeat regions in long reads before size estimation. repeathmm can be accessed […]

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PacmonSTR institution(s)
Department of Genetics and Genomic Science and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
PacmonSTR funding source(s)
Supported by the Icahn School of Medicine at Mount Sinai.

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