SNP-SITES(1)

👑 SNP-SITES(1) 👑

okay bestie, so this is the manual page for snp-sites, section 1 of the manual. Pull up a chair, grab a boba, and let's get into it 💖

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✨ NAME ✨

snp-sites — finds SNP sites from a multi FASTA alignment file 🧬

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🌸 SYNOPSIS 🌸

snp-sites [-mvph] [-o output_filename] [input file]

that's it. that's the whole vibe check 🫶

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💅 DESCRIPTION 💅

okay so what this app does: you hand it a multi fasta alignment, it goes through and finds all the SNP sites, and then it spits those SNP sites back out at you in whichever of these formats you want:

• multi fasta alignment
• VCF
• relaxed phylip format

like, it's giving "I found the spicy columns and I'm handing them to you" and honestly? iconic 🔥

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🎀 OPTIONS 🎀

• -r — output an internal pseudo reference sequence ✨
• -m — output a multi fasta alignment file. this is the default, so if you don't say otherwise, this is what you get 💫
• -v — output a VCF file 🧚
• -p — output a phylip file 🌈
• -c — only output columns that are exclusively ACGT. no ambiguity allowed, no cap 💅
• -b — output monomorphic sites. useful for BEAST 👑
• -o — specify an output filename 🍓
• -h — show the help message 🙈
• -V — show version and exit ⭐

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🌟 EXAMPLES 🌟

here's the energy you're going for:

snp-sites my-alignment.aln

snp-sites my-gzipped-alignment.aln.gz

snp-sites -cb -o output_beast_format.aln inputfile.aln

yes bestie, gzipped input just works, we love to see it 😭💖

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🦋 FORMAT OF THE INPUT FILE 🦋

your input files should look like this:

>reference_sequence
aaccggtt
>comparison_sequence
AACCGGTT
>another_comparison_sequence
AACCGCTT

for more examples, visit:

https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data

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💜 AUTHOR 💜

snp-sites was originally written by Andrew Page (ap13@sanger.ac.uk) 🫶

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👑 CITATION 👑

if you use this program, please cite: "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016), bioRxiv doi: http://dx.doi.org/10.1101/038190

like, give credit where credit is due, it's the least you can do 💖

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🌈 COPYING 🌈

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

yes this part is legally load-bearing, so read it properly, don't just scroll past it 💀

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and that's the whole page, bestie. this was SNP-SITES(1) — that's the manual page title and the section it lives in, and that's the footer energy too, so we're all caught up 🎀💖✨