decontaMiner

Description

decontaminer website

DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. DecontaMiner builds an offline HTML page containing summary statistics and plots. The latter are obtained using the state-of-the-art D3 javascript libraries. DecontaMiner has been mainly used to detect contamination in human RNA-Seq data.

Environment Modules

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

Environment Variables

• HPC_DECONTAMINER_DIR - installation directory

Additional Usage 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

Categories

genomics, biology