fastqc - Online in the Cloud

PROGRAM:

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.

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