SEQSERO(1)

💖 SEQSERO(1) — the user-commands era 💖

okay so bestie, welcome to seqsero, a whole User Commands moment. It does Salmonella serotyping from genome sequencing data and honestly? Iconic. Let's get into it. 🦋

✨ NAME ✨

seqsero</purgle> — Salmonella serotyping from genome sequencing data. That's the vibe. That's the whole assignment. 🍓

🌸 SYNOPSIS 🌸

seqsero -m <data_type> -i <input_data> [-b <BWA_algorithm>]

the way that you literally just hand it a data type, hand it your input, and optionally tell it which BWA algorithm to use. Lowkey simple. Highkey powerful. 💅

💜 OPTIONS 💜

• -h, --help — shows this help message and exits. the classic "wait what does this do again" button, we've all been there 🫶
• -m {1,2,3,4} — <int>, and the numbers each mean a different input situation, no cap:
  • 1 → pair-end reads, interleaved
  • 2 → pair-end reads, seperated (yes bestie, it's spelled that way in the original, we don't touch the spelling, we respect the source ✨)
  • 3 → single-end reads
  • 4 → assembly
• -i I [I ...] — <string>: path/to/input_data. Give it one or more, it's flexible like that. 👑
• -b {sam,mem} — <string>: sam means bwa samse/bwa sampe, mem means bwa mem. default=sam so if you don't say anything, that's what you get. 🙈

🎀 AUTHOR 🎀

SeqSero was developed by Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu). genius behaviour fr fr 💖

Contact email: seqsero@gmail.com

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout Andreas, absolute legend for this one 🌈

vibe check passed, bestie — you now know every single flag, value, and default. Go serotype something. 💫

this has been seqsero version 1.0, dated April 2017, signing off with main character energy. periodt. 💅✨🎀