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deconseq website  

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

Environment Modules

Run module spider deconseq to find out what environment modules are available for this application.

System Variables

  • HPC_DECONSEQ_DIR - installation directory

Additional Information

This module also includes PrinSeq.


If you publish research that uses deconseq you have to cite it as follows:

Schmieder R and Edwards R: Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 2011, 6:e17288.

Schmieder R and Edwards R: Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011, 27:863-864.