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QReport user manual

Obtains statistics from the reads quality of a fastq file. The binary output is then read by an Rmd script that generates a html visualization of the data.

Running the program

Usage C executable (in folder bin):

Usage: ./Qreport -i <INPUT_FILE.fq> -l <READ_LENGTH>
-o <OUTPUT_FILE> -t [NUMBER_OF_TILES] -q [MINQ]
-n [#_QUALITY_VALUES] -f [FILTER_STATUS]
Reads in a fq file (gz, bz2, z formats also accepted) and creates a
quality report (html file) along with the necessary data to create it
stored in binary format.
Options:
-v prints package version.
-h prints help dialog.
-i Input file [*fq|*fq.gz|*fq.bz2]. Mandatory option.
-l Read length. Length of the reads. Mandatory option.
-o Output file prefix (with NO extension). Mandatory option.
-t Number of tiles. Optional (default 96).
-q Minimum quality allowed. Optional (default 27).
-n Number of different quality values allowed. Optional (default 46).
-f Filter status: 0 original file, 1 file filtered with trimFilter,
2 file filtered with another tool. Optional (default 0).

Output description

NOTE If the data were sequenced on more than one lane, in Plots 3, 4 and 5 there will be a heatmap pro lane.

Example

An example is given in the folder examples/QReport_Sreport. To run an example, type,

$ cd example/Qreport_Sreport
$ mkdir run_test
$ cd run_test
$ ../../../bin/QReport -i ../test.fq.bz2 -l 51 -o my_test_output

and compare it with the provided run example, as specified in the README file under ./example/QReport_Sreport

Contributors

Paula Pérez Rubio

License

GPL v3 (see LICENSE.txt)