Sharq specifications


Unique identifier OMICS_26760
Name Sharq
Alternative name Single-cell Hierarchical Assignment of Reads and Quality control
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data A quality control (QC) report including plots and metrics.
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Stability Stable
Requirements STAR, subread, SGE, Set::Scalar, mismatch, Math::Combinatories, Regexp::Optimizer, platediagnostics, SCutils, uuutils
High performance computing Yes
Maintained Yes



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  • person_outline Frank Holstege <>
  • person_outline Tito Candelli <>
  • person_outline Philip Lijnzaad <>

Publication for Single-cell Hierarchical Assignment of Reads and Quality control

Sharq institution(s)
Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands; University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
Sharq funding source(s)
Supported by a grant from the European Research Council.

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