Provided by: fastqc_0.11.9+dfsg-2_all 
NAME
FastQC - high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
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.
--casava
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.
--extract
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.
--noextract
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.
--nogroup
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
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.
BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in
www.bioinformatics.babraham.ac.uk/bugzilla/
AUTHOR
This manpage was created using help2man by Andreas Tille <tille@debian.org> for the Debian
distribution but can be used by others as well.