NAME

       sickle - windowed adaptive trimming tool for FASTQ files using quality

SYNOPSIS

       sickle <command> [options]

DESCRIPTION

       ## Usage

       Sickle  has  two  modes to work with both paired-end and single-end reads: `sickle se` and
       `sickle pe`.

       Running sickle by itself will print the help:

           sickle

       Running sickle with either the "se" or "pe" commands will  give  help  specific  to  those
       commands:

           sickle se
           sickle pe

       ### Sickle Single End (`sickle se`)

       `sickle se` takes an input fastq file and outputs a trimmed version of that file.  It also
       has options to change the length and quality thresholds for trimming, as well as disabling
       5'-trimming and enabling truncation of sequences with Ns.

       #### Examples

           sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq
           sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40
           sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n
           sickle se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz

       ### Sickle Paired End (`sickle pe`)

       `sickle  pe` can operate with two types of input.  First, it can take two paired-end files
       as input and outputs two trimmed paired-end files as well as a "singles" file.  The second
       form  starts with a single combined input file of reads where you have already interleaved
       the reads from the sequencer.  In this form, you also supply a single output file name  as
       well  as a "singles" file.  The "singles" file contains reads that passed filter in either
       the forward or reverse direction, but not the other.  Finally, there is an option (-M)  to
       only  produce one interleaved output file where any reads that did not pass filter will be
       output as a FastQ record with a single "N" (whose quality value  is  the  lowest  possible
       based upon the quality type), thus preserving the paired nature of the data.  You can also
       change the length and quality thresholds for trimming, as well as disable 5'-trimming  and
       enable truncation of sequences with Ns.

       #### Examples

           sickle    pe    -f   input_file1.fastq   -r   input_file2.fastq   -t   sanger       -o
       trimmed_output_file1.fastq -p trimmed_output_file2.fastq     -s trimmed_singles_file.fastq

           sickle   pe   -f   input_file1.fastq   -r   input_file2.fastq   -t    sanger        -o
       trimmed_output_file1.fastq -p trimmed_output_file2.fastq     -s trimmed_singles_file.fastq
       -q 12 -l 15

           sickle   pe   -f   input_file1.fastq   -r   input_file2.fastq   -t    sanger        -o
       trimmed_output_file1.fastq -p trimmed_output_file2.fastq     -s trimmed_singles_file.fastq
       -n

           sickle   pe   -c    combo.fastq    -t    sanger    -m    combo_trimmed.fastq        -s
       trimmed_singles_file.fastq -n

           sickle   pe   -t   sanger   -g   -f   input_file1.fastq  -r  input_file2.fastq      -o
       trimmed_output_file1.fastq.gz        -p        trimmed_output_file2.fastq.gz            -s
       trimmed_singles_file.fastq.gz

           sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq

       Command: pe      paired-end sequence trimming se      single-end sequence trimming

       --help, display this help and exit --version, output version information and exit

AUTHOR

       Written by Nikhil Joshi, UC Davis Bioinformatics Core

COPYRIGHT

       Copyright  ©  2011  The Regents of University of California, Davis Campus.  sickle is free
       software and comes with ABSOLUTELY NO WARRANTY.  Distributed under the MIT License.

SEE ALSO

       The full documentation for sickle is maintained as a Texinfo  manual.   If  the  info  and
       sickle programs are properly installed at your site, the command

              info sickle

       should give you access to the complete manual.