smCounter specifications


Unique identifier OMICS_28672
Name smCounter
Alternative name smCounter2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline qiauser
  • person_outline Chang Xu
  • person_outline Yexun Wang
  • person_outline Xiujing Gu
  • person_outline Zhong Wu

Publications for smCounter

smCounter citation


A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] ncing errors can be effectively eliminated given enough read replications. The new challenge is DNA polymerase errors that an order of magnitude lower than sequencing errors. New variant callers like smCounter, MAGERI, and iDES have been developed to handle UMI data, and existing variant callers such as TVC have been upgraded with plug-ins for UMI. These tools have greatly pushed the limit of dete […]

smCounter institution(s)
Life Science Research and Foundation, Qiagen Sciences, Frederick, MD, USA
smCounter funding source(s)
Supported by R&D funding from QIAGEN Sciences.

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