qProfiler

qprofiler is a standalone Java app that takes in BAM or FASTQ files and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml).

While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs.

qProfiler uses the Picard library to access BAM files.

System Requirements

• Java 1.7
• Multi-core machine (ideally) and 12GB of RAM

Installation

• Download the qprofiler tar file
• Untar the tar file into a directory of your choice

You should see something like this:

[oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.tar.bz2
jopt-simple-3.2.jar
picard-1.110.jar
qcommon-0.1pre.jar
qio-0.1pre.jar
qmule-0.1pre.jar
qpicard-0.1pre.jar
qprofiler-1.0.jar
qvisualise-0.1pre.jar
sam-1.110.jar
[oholmes@minion0 test_adama_tools_data]$

Usage

java -jar qprofiler-1.0.jar 
     -input <full_path_to_input_bam>    
     -output <full_path_to_output_xml>
     -log <full_path_to_log_file>
     -ntC <number_of_consuming_threads> OPTIONAL
     -ntP <number_of_producing_threads> OPTIONAL
     -validation Possible values: {STRICT, LENIENT, SILENT}

For example, to run on a 16 core node:

java -jar qprofiler-1.0.jar \
     -input /sample_virus.BWA-backtrack.bam \
     -log /sample_virus.BWA-backtrack.bam.qp.log \
     -output /sample_virus.BWA-backtrack.bam.qp.xml \
     -ntP 4 -ntC 16

NOTE that BWA mapped bam files may need to be run with the optional parameter -validation SILENT otherwise Picard will throw an exception.