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MetaGPipe

MetaGPipe

MetaGPipe


MetaGPipe is a wrapper of the QIIME framework and FungalITSExtractor tool . It was especially designed to analyze PCR amplicons of fungal ITS regions sequenced with 454 technology. It was then successfully used with Illumina MiSeq reads.

MetaGPipe extracts ITS regions from input sequences and clusterizes them with uclust by using 97% similarity as a cutoff. Each cluster is designated by its most representative sequence. Taxonomic assignation is then performed by Blast against a filtered databank of ITS regions.

A reclustering step could be launched to study intra-cluster variability and highlight sequencing errors. In this case, we recommend to set the threshold to 1 (100% of similarity).

 

tool600

MetaGPipe workflow  

Context 

MetaGPipe was developped in the frame of the  FungiGrapeMetaG project . MetaGPipe results were presented during the 27th fungal genetics conference ( poster ).

Availability

MetaGPipe is available to download ( MetaGPipe source code ). The documentation describes how to install and run the pipeline. MetaGPipe requires several dependencies (programs and python modules). To avoid laborious install party, we provide a virtual machine "ready to run" on Virtualbox.

License

MetaGPipe is released under  the CeCILL license

Authors and Contributors

  • Françoise Alfama-Depauw
  • Joelle Amselem
  • Laetitia Brigitte
  • Angélique Gautier
  • Véronique Jamilloux
  • Nicolas Lapalu
  • Valérie Laval
  • Marc-Henri Lebrun

Contact and support

Contact us via email at urgi-support[[@]]versailles.inra.fr.


Access mode(s):

Downloadable

Update: 25 Nov 2015
Creation date: 05 Nov 2015