Provided by: fastqc_0.11.9+dfsg-2_all bug


       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.