DecontaMiner
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Description
A tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data.
Environment Modules
Run module spider decontaminer to find out what environment modules are available for this application.
System Variables
- HPC_DECONTAMINER_DIR - installation directory
Additional Information
The location of the external tools used by decontaMiner must be present in your configure.txt file (which is passed by the -c option when you run decontaMiner.sh). In order to use the pre-loaded tools in the cluster you should set the [ext_soft] sections to values similar to the following:
SAMTOOLS_EXEC=/apps/samtools/1.10/bin/samtools
FASTX_EXEC=/apps/fastx_toolkit/0.0.14/bin/fastq_quality_filter
BLASTN_EXEC=/apps/blast/ncbi/2.10.1/bin/blastn
SORTMERNA_EXEC=/apps/sortmerna/4.0/bin/sortmerna