One Codex lets you store, manage, and analyze genomic data. In doing so, the core concepts we tend to talk about are samples, analyses, and metadata.
A sample is a single FASTA/Q file, and it can contain genomic data from a single isolate or a complex mixed community (e.g., the human microbiome). One Codex optionally supports FASTA/Q files that are compressed using GZIP (i.e., files with the
Below is an example of a single sample as presented on the Samples page:
In addition to raw genomic sequence data, you can add more information describing each of your samples (e.g. sample name, sample type, location, etc.). Once you have that additional metadata entered into the platform, you can then use it to sort, filter, and organize your samples and analyses.
Some of the metadata on the sample shown above is:
The metadata for the sample above also contains three tags: arthiritis, complex, and stool.
One Codex can perform a number of different types of analysis – taxonomic classification, whole-genome alignment, etc. Each of those analyses may require different reference databases, algorithms, etc, and all of those components are wrapped up into a single analysis. We use standardized computational 'containers' to execute each analysis, which provides strong guarantees for reproducibility and bit-for-bit identical outputs.
Next: Dive into the results of metagenomic classification!