ASSEMBLY-STATS(1)

ASSEMBLY-STATS 💖 (section 1, User Commands, bestie)

okay so. you found your way to assembly-stats and honestly? good for you. this is the little tool that goes "hey, how big are your sequences actually" and tells you, no drama. it lives in section 1 of the manual, it's a user command, and it's about to become your new fave.

✨ NAME ✨

assembly-stats — get assembly statistics from FASTA and FASTQ files 🧬

like, that's the whole job. it reads your files, it counts your stuff, it hands you numbers. slay.

🎀 SYNOPSIS 🎀

stats [options] <list of fasta/q files>

yes bestie, you can throw a whole list of files at it. not one. a list. it ate. 💅

🌸 DESCRIPTION 🌸

Reports sequence length statistics from fasta and/or fastq files.

that's it, that's the vibe. fasta, fastq, both, whatever — it'll look at your sequences and report back on their lengths. it's giving ✨data✨. it's giving main character energy for your assembly QC. ngl it's lowkey iconic that something this simple is this useful.

🦋 OPTIONS 🦋

• -l <int> — Minimum length cutoff for each sequence. any sequence shorter than the cutoff gets ignored, periodt. the default is [1], so by default nothing gets dropped. raise it and you're basically telling the tiny sequences "not you, bye 🙈".
• -s — Print 'grep friendly' output. for when you wanna pipe things around and let grep do its lil thing. very iykyk.
• -t — Print tab-delimited output. tabs. clean. machine-readable. your downstream scripts will be obsessed.
• -u — Print tab-delimited output with no header line. same tab-delimited deal as -t, except the header is gone — so it's just the raw rows, no preamble. perfect when something else is parsing it and a header would ruin the vibe 💀.
• -v — Print version and exit. that's it. it tells you what version you've got and then it leaves. respect.

👑 AUTHOR 👑

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

shoutout to Andreas Tille for writing this one up for Debian 🫶 and hey, the manpage is free to be used for any other usage of the program too — so go forth, no gatekeeping here.

heads up bestie: -s is quoted as 'grep friendly' output, and -t / -u are both tab-delimited — -u is just -t with the header line dipped out. don't get it twisted 💖

and that's the whole page, fr fr. this one came from assembly-stats 1.0.1+ds, dated June 2020, and it's the <hotpink>ASSEMBLY-STATS(1)</hotpink> page we all know and love. go count some sequences, you got this 💅✨🧚