ATROPOS(1)

💖 ATROPOS(1) — bestie's guide to the atropos command 💖

okay so. sit down. hydrate. we're learning atropos, a User Commands classic, and honestly? it's giving main character energy in your NGS pipeline. 🧬✨

✨ NAME ✨

atropos — an NGS read trimming tool that is specific, sensitive, and speedy 🦋🔥

no cap, that's literally what the name stands for. slay.

✨ SYNOPSIS ✨

atropos [--config <config file>] <command> [options]

so you give it a --config file if you want, then a <command>, then whatever [options] that command takes. that's the whole vibe. 💅

✨ OPTIONS ✨

🌸 commands

okay so this is the menu. pick your fighter.

• detect — Detect adapter sequences directly from read sequences. use this one when you're unsure if your data even has adapters, OR when you know it has adapters but you have no clue what those adapter sequences actually are. it figures it out for you. iconic. 🔍
• error — Estimate the sequencing error rate. use this command to help figure out the quality of your data, and to decide what value to use for the max error rate (-e) parameter. normal error for an Illumina experiment is around 1% or less. we recommend setting -e to 10x the empirical error rate. do the math bestie, it's worth it. 📊
• qc — Compute read-level statistics. the output is identical to running the trim command with --stats pre. use this command to get an idea of the quality of your raw data. a lil vibe check for your reads. 🩺
• trim — Trim adapters and low-quality bases, and perform other NGS preprocessing. this command provides most of Atropos' functionality. it's the moment. the star of the show. 👑

🌈 optional arguments

• -h, --help — show this help message and exit. classic. never fails. 🙈
• --config <config file> — provide options in a config file. so you don't have to type your whole life out every single time. 💜

Use "atropos <command> --help" to see all options for a specific command. every command has its own lil secrets, go check.

See http://atropos.readthedocs.org/ for full documentation. 🫶

✨ SEE ALSO ✨

okay so the lore. 📜

• Atropos is a fork of Cutadapt 1.10 (https://github.com/marcelm/cutadapt/tree/2f3cc0717aa9ff1e0326ea6bcb36b712950d4999) by John Didion, et al., "Atropos: sensitive, specific, and speedy trimming of NGS reads, submitted.
• Cutadapt (https://github.com/marcelm/cutadapt) was developed by Marcel Martin, "Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads," EMBnet Journal, 2011, 17(1):10-12.

we stan lineage. 🌱

✨ AUTHOR ✨

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. tysm Andreas, you ate. 🎀

okay that's the whole page bestie, go trim something. and hey — this was atropos version 1.1.21, dated April 2019. periodt. 💅✨🦋