Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.

Features

  • shotgun or amplicon (e.g. 16S rRNA) read libraries
  • omics support to generate genomic, transcriptomic, proteomic, metagenomic, metatranscriptomic or metaproteomic datasets
  • arbitrary read length distribution and number of reads
  • simulation of PCR and sequencing errors (chimeras, point mutations, homopolymers)
  • support for paired-end (mate pair) datasets
  • specific rank-abundance settings or manually given abundance for each genome, gene or protein
  • creation of datasets with a given richness (alpha diversity)
  • related datasets can share a variable number of genomes (beta diversity)
  • modeling of the bias created by varying genome lengths or gene copy number
  • profile mechanism to store preferred options
  • available to biologists or power users through multiple interfaces: GUI, CLI and API

Project Activity

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Categories

Bio-Informatics

License

GNU General Public License version 2.0 (GPLv2)

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User Reviews

  • Biogrinder is the best! Thanks.
    1 user found this review helpful.
  • Great App ,Excellent
  • great, thanks
  • Not working on Windows vista x64
  • Not operating on Windows 7
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Additional Project Details

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

Perl

Related Categories

Perl Bio-Informatics Software

Registered

2008-11-03