AUGUR(1)

👑 AUGUR — like, the manual page, but make it make sense 💅

okay bestie, gather round, because this is augur and she is that girl. AUGUR(1) energy fr fr. This is a User Commands page, and it's giving "bioinformatics toolkit that actually slaps." Let's get into it. 🦋

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✨ NAME ✨

augur — pipeline components for real-time virus analysis 🦠✨

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🌸 DESCRIPTION 🌸

so the vibe is:

usage: augur [-h]

       {parse, index, filter, mask, align, tree, refine, ancestral,
       translate, reconstruct-sequences, clades, traits,
       sequence-traits, lbi, distance, titers, frequencies, export,
       validate, version, import, measurements} ...

Augur: A bioinformatics toolkit for phylogenetic analysis. periodt. that's the whole assignment. 👑

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🎀 positional arguments 🎀

like, you literally have to pick one of these, bestie. no skipping:

{parse, index, filter, mask, align, tree, refine, ancestral, translate, reconstruct-sequences, clades, traits, sequence-traits, lbi, distance, titers, frequencies, export, validate, version, import, measurements}

and now the roll call, no cap, every single one of them:

• parse — Parse delimited fields from FASTA sequence names into a TSV and FASTA file. 🍓
• index — Count occurrence of bases in a set of sequences. counting era, honestly.
• filter — Filter and subsample a sequence set. it's giving ✨curation✨
• mask — Mask specified sites from a VCF or FASTA file. bye bye sites 💀
• align — Align multiple sequences from FASTA. line them up, slay.
• tree — Build a tree using a variety of methods. 🌳 multiple methods? versatile queen.
• refine — Refine an initial tree using sequence metadata. glow-up for your tree 💅
• ancestral — Infer ancestral sequences based on a tree. looking back in time, iconic.
• translate — Translate gene regions from nucleotides to amino acids. glow-up but molecular 🧬
• reconstruct-sequences — Reconstruct alignments from mutations inferred on the tree. (no period, she's mysterious like that 😌)
• clades — Assign clades to nodes in a tree based on amino-acid or nucleotide signatures. assign bestie, you got this.
• traits — Infer ancestral traits based on a tree. the ancestors spilled 🫖
• sequence-traits — Annotate sequences based on amino-acid or nucleotide signatures. annotate & serve.
• lbi — Calculate LBI for a given tree and one or more sets of parameters. math girlies rise 🧮
• distance — Calculate the distance between sequences across entire genes or at a predefined subset of sites. how far apart? we'll see 💅
• titers — Annotate a tree with actual and inferred titer measurements. actual AND inferred, she does both.
• frequencies — infer frequencies of mutations or clades. lowercase title, lowercase chill. 😎
• export — Export JSON files suitable for visualization with auspice. JSON out, vibes in.
• validate — Validate files related to augur consumption or export. the friend who checks the group chat before you send it 🫶
• version — Print the version of augur. quick lil flex.
• import — Import analyses into augur pipeline from other systems. come on in, the pipeline is fine 🏠
• measurements — Create JSON files suitable for visualization within the measurements panel of Auspice. it's giving dashboard glamour ✨

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💖 options 💖

only one, but she's essential, and she's carrying the whole section on her back:

• -h, --help — show this help message and exit. the classic. the icon. 🌈

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🦋 AUTHOR 🦋

This manpage was written by Étienne Mollier for the Debian distribution and can be used for any other usage of the program. shoutout to Étienne, fr fr, realest one for this 🫶✨

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lowkey reminder bestie: every flag, every subcommand, every weird little detail up there is canon. I didn't make any of it up and you shouldn't either. 💀

okay that's the page!! 💖 augur version 16.0.1, dated June 2022, living her life in the AUGUR(1) section of your friendly neighborhood User Commands manual. bye bestie, go build a tree 🌳👑✨