ARIBA(1)

📦
version 2.14.7 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 NAME 💖

okay so bestie, welcome to ariba — it literally stands for Antibiotic Resistance Identification By Assembly ✨ and it's the moment.

🌸 SYNOPSIS 🌸

ariba <subtool> [options]

that's it. that's the whole vibe. a subtool plus options, go off 👑

🦋 DESCRIPTION 🦋

ariba is the main executable for the ARIBA software — the tool that finds antibiotic resistance genes by running local assemblies. no cap, that's the whole job.

so like, generally the way it goes: your input is a FASTA file of reference sequences (and yes it can be a lil mix — genes and noncoding sequences, she's flexible 💅) plus paired sequencing reads. then ARIBA reports back which of those reference sequences were actually found, plus the full tea on how good the assemblies were and any variants hanging out between the sequencing reads and the reference sequences. obsessed honestly.

the actual functionality? provided by the subtools, listed right below 👇

🎀 Subtools

  • getref — download reference data 📥
  • prepareref — prepare reference data for input to "run"
  • run — run the ARIBA local assembly pipeline 🏃♀️
  • refquery — get cluster or sequence info from prepareref output
  • reportfilter — Filter report.tsv file
  • summary — summarise multiple reports made by "run"
  • flag — translate the meaning of a flag 🚩
  • aln2meta — converts multi-aln fasta and SNPs to metadata
  • test — run small built-in test dataset 🧪
  • version — get versions and exit

💜 Subtool help

you can literally just run

ariba <subtool> --help

to show more info about how to run each individual subtool. it's giving helpful. it's giving ✨supportive✨.

😭 BUGS

found a bug? please please please report it to the ARIBA issue tracker, bestie, they wanna know:

https://github.com/sanger-pathogens/ariba/issues

fr fr, don't suffer in silence, the maintainers are literally waiting to help 🫶

and that's the page!! this was ariba(1) — the ARIBA manual, in all her glory — dated and versioned right there in the footer, so if you're reading this scroll back down and check the bottom of the original, mwah 💋 thanks for coming to my ted talk, slay, periodt 🎀✨

📦 where this page comes from