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.