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Grinder

5.0 Stars (33)
16 Downloads (This Week)
Last Update:
Download Grinder-0.5.4.tar.gz
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Description

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

Grinder Web Site

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

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User Ratings

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User Reviews

  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Biogrinder is the best! Thanks.

    Posted 06/12/2013
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Great App ,Excellent

    Posted 02/09/2013
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Excellent software, thanks to everyone involved in its development!

    Posted 11/07/2012
  • 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    very good project

    Posted 11/07/2012
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Additional Project Details

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

Perl

Registered

2008-11-03

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