You can see how we use FastQC to quality check raw reads in our protocol here

-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.
--nano          Files come from naopore sequences and are in fast5 format. In
                this mode you can pass in directories to process and the program
                will take in all fast5 files within those directories and produce
                a single output file from the sequences found in all files.                    
--nofilter      If running with --casava then don't remove read flagged by
                casava as poor quality when performing the QC analysis.
--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
-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!
--min_length    Sets an artificial lower limit on the length of the sequence
                to be shown in the report.  As long as you set this to a value
                greater or equal to your longest read length then this will be
                the sequence length used to create your read groups.  This can
                be useful for making directly comaparable statistics from 
                datasets with somewhat variable read lengths.
-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.

-a              Specifies a non-default file which contains the list of
--adapters      adapter sequences which will be explicity searched against
                the library. The file must contain sets of named adapters
                in the form name[tab]sequence.  Lines prefixed with a hash
                will be ignored.
-l              Specifies a non-default file which contains a set of criteria
--limits        which will be used to determine the warn/error limits for the
                various modules.  This file can also be used to selectively 
                remove some modules from the output all together.  The format
                needs to mirror the default limits.txt file found in the
                Configuration folder.
-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 7 if not specified.

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

-d --dir				Selects a directory to be used for temporary files written when
								generating report images. Defaults to system temp directory if
								not specified.