FASTQC(1)                        User Commands                       FASTQC(1)

       FastQC - high throughput sequence QC analysis tool


              fastqc seqfile1 seqfile2 .. seqfileN

              fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]

              [-c contaminant file] seqfile1 .. seqfileN

              FastQC reads a set of sequence files and produces from each one
              a quality control report consisting of a number of different
              modules, each one of which will help to identify a different
              potential type of problem in your data.

              If no files to process are specified on the command line then
              the program will start as an interactive graphical application.
              If files are provided on the command line then the program will
              run with no user interaction required.  In this mode it is
              suitable for inclusion into a standardised analysis pipeline.

              The options for the program as as follows:

       -h --help
              Print this help file and exit

       -v --version
              Print the version of the program and exit

       -o --outdir
              Create all output files in the specified output directory.
              Please note that this directory must exist as the program will
              not create it.  If this option is not set then the output file
              for each sequence file is created in the same directory as the
              sequence file which was processed.

              Files come from raw casava output. Files in the same sample
              group (differing only by the group number) will be analysed as a
              set rather than individually. Sequences with the filter flag set
              in the header will be excluded from the analysis.  Files must
              have the same names given to them by casava (including being
              gzipped and ending with .gz) otherwise they won't be grouped
              together correctly.

              If set then the zipped output file will be uncompressed in the
              same directory after it has been created.  By default this
              option will be set if fastqc is run in non-interactive mode.

       -j --java
              Provides the full path to the java binary you want to use to
              launch fastqc. If not supplied then java is assumed to be in
              your path.

              Do not uncompress the output file after creating it.  You should
              set this option if you do not wish to uncompress the output when
              running in non-interactive mode.

              Disable grouping of bases for reads >50bp. All reports will show
              data for every base in the read.  WARNING: Using this option
              will cause fastqc to crash and burn if you use it on really long
              reads, and your plots may end up a ridiculous size.  You have
              been warned!

       -f --format
              Bypasses the normal sequence file format detection and forces
              the program to use the specified format.  Valid formats are
              bam,sam,bam_mapped,sam_mapped and fastq

       -t --threads
              Specifies the number of files which can be processed
              simultaneously.  Each thread will be allocated 250MB of memory
              so you shouldn't run more threads than your available memory
              will cope with, and not more than 6 threads on a 32 bit machine

       -c     Specifies a non-default file which contains the list of

              contaminants to screen overrepresented sequences against.  The
              file must contain sets of named contaminants in the form
              name[tab]sequence.  Lines prefixed with a hash will be ignored.

       -k --kmers
              Specifies the length of Kmer to look for in the Kmer content
              module. Specified Kmer length must be between 2 and 10. Default
              length is 5 if not specified.

       -q --quiet
              Suppress all progress messages on stdout and only report errors.

              Any bugs in fastqc should be reported either to
     or in

              This manpage was created using help2man by Andreas Tille
              <> for the Debian distribution but can be used
              by others as well.

FastQC v0.10.1                   November 2012                       FASTQC(1)