参考网站https://anaconda.org/bioconda/fastqc

conda install -c bioconda fastqc

fastqc教程参考网站：https://www.bioinformatics.babraham.ac.uk/projects/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/