Program options for fastqc: FastQC - A 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. --nano Files come from nanopore 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 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! --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. BUGS Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk or in www.bioinformatics.babraham.ac.uk/bugzilla/ ---------------------------------------------- Program options for multiqc: Usage: multiqc [OPTIONS] Main MultiQC run command for use with the click command line, complete with all click function decorators. To make it easy to use MultiQC within notebooks and other locations that don't need click, we simply pass the parsed variables on to a vanilla python function. Options: -f, --force Overwrite any existing reports -d, --dirs Prepend directory to sample names -dd, --dirs-depth INTEGER Prepend [INT] directories to sample names. Negative number to take from start of path. -s, --fullnames Do not clean the sample names (leave as full file name) -i, --title TEXT Report title. Printed as page header, used for filename if not otherwise specified. -b, --comment TEXT Custom comment, will be printed at the top of the report. -n, --filename TEXT Report filename. Use 'stdout' to print to standard out. -o, --outdir TEXT Create report in the specified output directory. -t, --template [default|default_dev|geo|sections|simple] Report template to use. --tag TEXT Use only modules which tagged with this keyword, eg. RNA --view-tags, --view_tags View the available tags and which modules they load -x, --ignore TEXT Ignore analysis files (glob expression) --ignore-samples TEXT Ignore sample names (glob expression) --ignore-symlinks Ignore symlinked directories and files --sample-names PATH File containing alternative sample names -l, --file-list Supply a file containing a list of file paths to be searched, one per row -e, --exclude [module name] Do not use this module. Can specify multiple times. -m, --module [module name] Use only this module. Can specify multiple times. --data-dir Force the parsed data directory to be created. --no-data-dir Prevent the parsed data directory from being created. -k, --data-format [tsv|json|yaml] Output parsed data in a different format. Default: tsv -z, --zip-data-dir Compress the data directory. -p, --export Export plots as static images in addition to the report -fp, --flat Use only flat plots (static images) -ip, --interactive Use only interactive plots (HighCharts Javascript) --lint Use strict linting (validation) to help code development --pdf Creates PDF report with 'simple' template. Requires Pandoc to be installed. --no-megaqc-upload Don't upload generated report to MegaQC, even if MegaQC options are found -c, --config PATH Specific config file to load, after those in MultiQC dir / home dir / working dir. --cl-config, --cl_config TEXT Specify MultiQC config YAML on the command line -v, --verbose Increase output verbosity. -q, --quiet Only show log warnings --no-ansi Disable coloured log output --version Show the version and exit. -h, --help Show this message and exit. ----------------------------------------------