GSP incorporate the Bayesian framework and EM algorithm for the genome size prediction without de novo assembling. This clever approach use the l-mer hash for the basic frequency statistic, then extended the l-mer frequency table into BE & EM iterator for genome size estimating. The software is written in C and supports the FASTQ/FASTA format as the input files. The software not only supports the simulating data but also supports the real data set with an extra error model.
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      Estimate your genome size in minutes with GSP !

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     Main Features
  • fast calculate the K-mer frequency of the genome size.
  • Bayesian framework for frequency estimating
  • EM iterative algorithm for the genome size predition.
  • work with  simualted data and real data with an extra error model
  • specially advantage even reduce sequence data szie lower to 2-4 fold cases
     
     What new features would you like to see in a future release? - Tell us right now!


If you hope to known the genome size before de novo assembing, this is a definite must have. It is beyond simple!
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(An Efficient l-mer frequency genome size predictor)


Copyright, 2009 - 2010, The Zhejiang University, China.  All Rights reserved.

Permission granted to download and use GSP freely for academics.  Any restrictions to use by non-academics are License need. Contact Zhejiang University Ph.D. Email: shangood@zju.edu.cn.

Copyright @ 2009-2010 Zhejiang University. All Rights Reserved.

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