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SimBA

SimBA

SimBA consists of a set of tools for benchmarking and evaluation of RNA-seq pipelines. Set contains two tools, SimCT and BenchCT. SimCT simulates RNA-seq data sets, and BenchCT does the benchmarking by comparing output from an RNA-seq pipeline against the simulated data.

Topic

RNA-seq

Details

  • Operation: Modelling and simulation; RNA-Seq analysis
  • Input: FASTA
  • Output: -
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux; Mac OS X
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: Fondation pour la Recherche Médicale, SATT AxLR, la Région Occitanie, and Montpellier Métropole Méditerranée. Institute of Computational Biology, Investissement d’Avenir.
  • Contact: cractools-bugs _at_ lists.gforge.inria.fr
  • Collection: -

Publications

Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N "SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines." BMC Bioinformatics. 2017 Sep 29;18(1):428. https://doi.org/10.1186/s12859-017-1831-5
PMID: 28969586
PMCID: PMC5623974


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