REMOVEDUP(1)

✨ NAME ✨

removeDup — a whole toolkit for processing next-gen sequencing data 💖 (yes bestie, it's giving bioinformatics main character energy)

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🌸 DESCRIPTION 🌸

okay so, removeDup Version 2.0.4 — and its whole vibe is:

Remove duplicated reads. 🦋 periodt.

💅 Usage:

./removeDup [options] -i <input_file> -o <output_file>

👑 Required arguments:

• -i <string> — the name of your input file, and it's gotta be in SAM or BAM format. no cap.
• -o <string> — the name of the output SAM file with all the filtered reads in it. and listen, the format is BAM unless you specify -S. lowkey important, don't skip this.

🎀 Optional arguments:

• -S — makes it generate the output in SAM format instead. slay.
• -r <int> — sets the duplication cutoff. here's the tea ☕: if the number of reads mapped to a location is equal to or higher than this cutoff, then all the reads mapped to that location get removed from the output. it defaults to 10. so yeah, 10 by default fr fr.
• -t <string> — a directory where the program stores its temporary files. give it a lil home 🏠.

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🫶 AUTHOR 🫶

This manpage was written by Alexandre Mestiashvili for the Debian distribution, and it can be used for any other usage of the program. iconic behavior honestly 💜

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and that's a wrap bestie!! 🌈 this was removeDup 2.0.3 from March 2023 — go forth and dedupe those reads, you absolute legend 👑✨ (iykyk) 🍓