SICKLE(1)

💖 sickle(1) — the windowed adaptive trimming tool for FASTQ files using quality 💖

okay bestie, welcome to the <rainbow>sickle</rainbow> manual page 💅 it's a User Commands situation, and we're about to make FASTQ trimming feel like a group chat glow-up. no cap, this tool is iconic.

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🌸 NAME 🌸

<sickle>sickle</sickle> — windowed adaptive trimming tool for FASTQ files using quality ✨

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🎀 SYNOPSIS 🎀

sickle <command> [options]

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✨ DESCRIPTION ✨

💜 Usage 💜

Sickle has two modes, one for paired-end and one for single-end reads, and the way it works is literally just sickle se and sickle pe. pick your fighter 🫶

Running sickle all by itself will print the help:

sickle

And running sickle with either the se or pe commands gives you help specific to those commands:

sickle se
sickle pe

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🦋 Sickle Single End (sickle se) 🦋

<pink>sickle se</pink> 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, plus options for disabling 5'-trimming and enabling truncation of sequences with Ns. so many little toggles, so much power 💖

⭐ 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

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🌈 Sickle Paired End (sickle pe) 🌈

<pink>sickle pe</pink> can operate with two types of input, okay so listen:

First form — it can take two paired-end files as input, and it outputs two trimmed paired-end files plus a "singles" file.

Second form — it starts with a single combined input file of reads where you've already interleaved the reads from the sequencer. in this form you also supply a single output file name, plus a "singles" file.

The "singles" file contains reads that passed filter in either the forward or reverse direction, but not the other. periodt.

Finally, there's 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. chef's kiss, honestly 👑

You can also change the length and quality thresholds for trimming, as well as disable 5'-trimming and enable truncation of sequences with Ns. same energy as se, double the files 💅

🎀 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

And here's the command rundown, exactly as the tool lays it out:

Command: pe      paired-end sequence trimming
se      single-end sequence trimming

--help, display this help and exit
--version, output version information and exit

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💜 AUTHOR 💜

Written by Nikhil Joshi, UC Davis Bioinformatics Core 🫶

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🌸 COPYRIGHT 🌸

Copyright © 2011 The Regents of University of California, Davis Campus.

sickle is free software and comes with ABSOLUTELY NO WARRANTY. 🚨 (like, genuinely, zero warranty, bestie — read that twice)

Distributed under the MIT License.

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🦋 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. go read it, it's giving ✨

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🌟 cute little sign-off: this whole thing is sickle version 1.33, dated June 2020. 💖 mwah, go trim some reads, you've got this. 🎀🦋💅