SMS-seq  🧬 → ☎️ → 🦠

Second- and third-generation sequencing have made it fast, cheap, and easy to characterize complex metagenomic samples. As a consequence, researchers increasingly find themselves sequencing a sample and then asking the question, “what the heck is this?”

And, more and more, they’re asking this question while in environments that are wholly unsuitable for computational analysis – think crowded subway trains, space stations, the middle of an Ebola outbreak, and a Dante-esque giant burning crater in Turkmenistan known affectionately as the “Door to Hell”. These are no place for a computational biologist!

To address this glaring gap in truly portable sequencing data analysis, we’re excited today to announce our new, breakthrough SMS-seq service.

Announcing SMS-seq

SMS-seq, or short message service-based (SMS) sequence analysis is – to our knowledge – the world’s first metagenomics data analysis tool that works on a dumbphone. Best of all, it’s completely free to use and may even work when you only have 1 bar of service!

So how do I get started?

Glad you asked! Getting started with SMS-seq is, relative to other bioinformatics tools, quite simple.

  • Step 1: Ensure that you have an up-to-date installation of Anaconda’s bioconda package manager, Homebrew or Linuxbrew (brew), and the latest and greatest versions of any relevant compilers (gcc, gfortran, clang, ghc, etc.).
  • Step 2: Next, install R and as many of these awesome R packages as you find prudent (we’ll wait).
  • Step 3: Next you’ll need to investigate the encoding for text messages and prepare to send our servers a message using curl (or httpie if you’re a hipster).
  • Step 4: Just kidding, you don’t need to do any of this! Just skip to the next paragraph already!

No really, all you need to do is shoot us a text!1 Text your favorite, bizarre, or otherwise obscure microbial nucleotide sequences to us at 1-415-942-6339 (1-415-94CODEX).

We need at least 32 bases and will classify your sequence against our reference database of >100K microbial genomes. Here’s the SMS-seq in action:

As always, we’re working tirelessly to bring you better bioinformatics tools, even when that’s to an ever-broader set of devices in ever-more-unsuitable-for-bioinformatics locales. We hope you enjoy the groundbreaking SMS-seq technology, and please get in touch if you have other ideas to make microbial genomics even more accessible!

1 Standard data and messaging rates may apply. Various smartphones (or dumbphones) are available and smaller than a stapler. Also, please don’t text (or fax) us any medical information.

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