Usage

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