---
name: "sickle"
section: "1"
platform: "linux"
package: "sickle"
version: "1.33+git20150314.f3d6ae3-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sickle"
---

# sickle(1)

windowed adaptive trimming tool for FASTQ files using quality

## 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.