qprofiler (Latest)
qprofiler provides quality control reporting for next-generation sequencing(NGS). qprofiler takes FASTQ, BAM/SAM, FASTA, QUAL,GFF3, MA and VCF files as input and outputs an XML file containing summary statistics tailored to the input file type. If no output file is specified then the default output file name will be used: 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 via the Charts javascript library developed by Google. qvisualise exists as a standalone program but it is also integrated into qprofiler so a HTML file will always be output by qprofiler unless the --nohtml tag is used. The HTML file name is based on the XML output filename with the extension .html appended.
Installation
qprofiler requires java 21, multi-core machine (ideally) and 5GB of RAM
- To do a build of qprofiler, first clone the adamajava repository using "git clone":
git clone https://github.com/AdamaJava/adamajava
Then move into the adamajava folder:
cd adamajava
Run gradle to build qprofiler and its dependent jar files:
./gradlew :qprofiler:build
This creates the qprofiler jar file along with dependent jars in the qprofiler/build/flat folder
Running qprofiler
- To run qprofiler, you need to supply an output, a log file and one or more inputs:
usage: java -jar qprofiler.jar --input <input file> --output <output xml file> --log <log file> [options]
Option Description
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Option Description
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-h, --help Show usage and help.
--include Deprecated, Visualisation for SOLiD platform.
--index Opt, A bai index file. Def=null.
--input Req, Input file in FASTQ, BAM/SAM or VCF format, also
support FA, MA, QUAL, FASTA, GFF and GFF3 format.
--log Req, Log file.
--loglevel Opt, Logging level [INFO,DEBUG], Def=INFO.
--nohtml Opt, No html output will be generated if this option is
set.
--output Opt, XML output which containing basic summary statistics.
Def="qprofiler.xml".
--records <Integer> Opt, Only process the specified number of records from the
beginning of the BAM file
--tags Opt, Specify user defined tags in SAM/BAM file, which
support printable string type, eg.["ZC", "XY"].
--tagsChar Opt, Specify user defined tags in SAM/BAM file, which
support Printable character type, eg.["ZC", "XY"].
--tagsInt Opt, Specify user defined tags in SAM/BAM file, which
support Signed integer type, eg.["ZC", "XY"].
--threads-consumer <Integer> Opt, Number of threads to process inputed BAM records.
Def=0 (run in single thread mode).
--threads-producer <Integer> Opt, Number of threads to read the indexed BAM file. This
option will ignored without positive value of "threads-
consumer". Def=1.
--validation Opt, BAM record validation stringency [STRICT,LENIENT,
SILENT]. Def=LENIENT.
--version Show version number.