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.