DeconSeq¶

Description¶

The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination 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.

Environment Variables¶

HPC_DECONSEQ_DIR - installation directory
HPC_DECONSEQ_BIN - executable directory
HPC_DECONSEQ_DOC - documentation directory

Additional Usage Information¶

This module also includes PrinSeq.

Citation¶

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

Schmieder, R., & Edwards, R. (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLOS ONE, 6(3), e17288. https://doi.org/10.1371/journal.pone.0017288

Schmieder, R., & Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27(6), 863–864. https://doi.org/10.1093/bioinformatics/btr026

Categories¶

biology, phylogenetics