Automated Drag-and-Drop Microbiome Analysis for Oxford Nanopore Sequencers

We just launched a brand new feature that’s been near the top of the list of requests for a while: now, when you want to upload FASTQ files from ONT sequencers but each file is split into several parts, we’ll automatically detect the parts and concatenate the files together for you!

Oxford Nanopore (ONT from here on out) has done a fantastic job of making metagenomic sequencing more accessible through its range of easy to use, affordable sequencers. We’ve had first class support for ONT sequencing data for years now, but it’s always been a pain to have to concatenate the different partial FASTQ files for each barcode separately before uploading them to One Codex.

While the output format of ONT’s basecaller can be fully configured, labs commonly leave the default settings, resulting in 100s of small files rather than one per sample. This requires an extra step between sequencing and analysis. We felt like we weren’t holding up our end of the bargain by having One Codex be drag-and-drop, one-click easy to use! So now, we’ll detect when you might have multiple FASTQ files for the same barcode and automatically concatenate them for you as part of the upload process. That way you just drag and drop all of your files into One Codex in your browser, and we’ll make sure you get a single, well-organized sample uploaded into your account.

We’ll even let you know if we’re missing a partial file that we expect. This feature will work out of the box with default naming schemes for these files, since we’re just looking for a shared filename with an auto-incrementing suffix in your filenames (like my_barcode_part_1.fastq.gz, my_barcode_part_2.fastq.gz). If you want to disable this behaviour, you can just toggle the “Auto-interleave?” switch off before you drag and drop your files.

CLI support

In addition to the web application, we now also auto-detect and auto-concatenate ONT files when you upload via our command line interface. That means you can just point the CLI at a folder of FASTQ files and it will figure out what to interleave and what to concatenate. By default, you’ll be prompted to confirm what’s going to be interleaved and concatenated, but you can also pass the --no-prompt flag to proceed without prompting.

Thanks for reading, and we hope this sparks a little bit of joy while you’re analyzing your metagenomics data ✨🪄

As always, you can stay up to date with new feature releases by subscribing to the blog or checking out our ✨brand new changelog ✨. We’d also love to hear your ideas for what we should build next at hello@onecodex.com