Grinder 0.5.2

Tool for generating random amplicon and shotgun libraries
Grinder is a program that allows you to create artificial random shotgun and amplicon sequence libraries.

The libraries generated are based on reference sequences in a FASTA file. Grinder can produce metagenomes, pyrotag datasets or shotgun sequencing projects, which can be used to test the accuracy of bioinformatic tools or help decide between alternative sequencing methods in an experiment.

Main features:

  • arbitrary number of reads and read length distribution
  • simulation of various PCR and sequencing errors: chimeras, point mutations, homopolymers
  • random shotgun library or amplicon library (e.g. 16S)
  • support for creating paired-end shotgun datasets
  • specific rank-abundance or manually specified abundance for each genome
  • creation of independent datasets, that do not share any genomes
  • modeling of the bias created by different genome lengths
  • forbidden characters
  • alpha and beta diversity requirements

last updated on:
April 28th, 2013, 15:22 GMT
file size:
207 KB
price:
FREE!
developed by:
Florent Angly
license type:
GPL 
operating system(s):
Windows All
category:
C: \ Science / CAD

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What's New in version 0.4.8
  • Fixed bug when making amplicon reads using specified relative abundances based on genomes with multiple amplicons.
  • Usage message improvements.
  • Delegated some operations to dedicated modules.
read full changelog

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