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    se    --fastq-file   input_file.fastq   --qual-type   sanger   --output-file
       trimmed_output_file.fastq

       ### 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

           sickle pe --pe-file1 input_file1.fastq --pe-file2 input_file2.fastq --qual-type sanger
       --output-pe1     trimmed_output_file1.fastq     --output-pe2    trimmed_output_file2.fastq
       --output-single trimmed_singles_file.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.