.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH SICKLE "1" "October 2016" "sickle version 1.33" "User Commands"
.SH NAME
sickle \- windowed adaptive trimming tool for FASTQ files using quality
.SH SYNOPSIS
.B sickle
\fI\,<command> \/\fR[\fI\,options\/\fR]
.SH 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
.PP
Command:
pe      paired\-end sequence trimming
se      single\-end sequence trimming
.PP
\fB\-\-help\fR, display this help and exit
\fB\-\-version\fR, output version information and exit
.SH AUTHOR
Written by Nikhil Joshi, UC Davis Bioinformatics Core
.SH COPYRIGHT
Copyright \(co 2011 The Regents of University of California, Davis Campus.
sickle is free software and comes with ABSOLUTELY NO WARRANTY.
Distributed under the MIT License.
.SH "SEE ALSO"
The full documentation for
.B sickle
is maintained as a Texinfo manual.  If the
.B info
and
.B sickle
programs are properly installed at your site, the command
.IP
.B info sickle
.PP
should give you access to the complete manual.