SMaSH

SMaSH is a benchmarking methodology designed for evaluating germline variant calling algorithms in next-generation sequencing data. The methodology includes the generation of synthetic datasets, organization and interpretation of existing benchmarking data, and the proposal of accuracy and computational performance metrics.

Topic

Genetics;Protein variants;Genomics

Detail

  • Operation: Data handling

  • Software interface: Command-line user interface

  • Language: Python

  • License: BSD 2-Clause "Simplified" License

  • Cost: Free

  • Version name: v1.0

  • Credit: NSF, NIH National Research Service Award Trainee appointment, NSF CISE Expeditions award, DARPA XData Award, Amazon Web Services, Google, SAP, Cisco, Clearstory Data, Cloudera, Ericsson, Facebook, FitWave, General Electric, Hortonworks, Huawei, Intel, Microsoft, NetApp, Oracle, Samsung, Splunk, VMware, WANdisco and Yahoo!.

  • Input: -

  • Output: -

  • Contact: Ameet Talwalkar ameet@cs.berkeley.edu, David Patterson pattrsn@cs.berkeley.edu

  • Collection: -

  • Maturity: -

Publications

  • SMaSH: a benchmarking toolkit for human genome variant calling.
  • Talwalkar A, et al. SMaSH: a benchmarking toolkit for human genome variant calling. SMaSH: a benchmarking toolkit for human genome variant calling. 2014; 30:2787-95. doi: 10.1093/bioinformatics/btu345
  • https://doi.org/10.1093/bioinformatics/btu345
  • PMID: 24894505
  • PMC: PMC4173010

Download and documentation

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