fastqc(1)
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.
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