One platform for metagenomics.
Fathom your sequencing data.
Most tools align your reads to one reference, then the next, then the next: a slow chain of sequential passes. Fathom's sample composition module is different: it compares against all references simultaneously, delivering greater accuracy and immense speed in a single pass.
Each sample resolves into four groups: human, bacteria, virus, and fungi. Reads matching more than one group equally are reported as ambiguous, and reads with no confident match as unknown. Every read is counted once, so a sample always adds up to 100%.
Fathom uses fastp to provide read-level quality metrics: base quality, duplication, adapter trimming, mean read length, insert size, etc. In addition, sample composition also provides a unique and powerful way to QC a sample. It allows you to rapidly see if there are unexpected contaminants or if the composition contains more of a particular kingdom or host than is expected.
Fathom screens your sample against a wide range of bacterial, viral, and fungal human pathogens, and reports each one it finds with per-gene coverage you can drill into.
Where the strain matters, Fathom types it: distinguishing SARS-CoV-2 lineages and influenza subtypes such as A (H1N1), so a positive call comes with the resolution you need.
Its detection methods draw on the best bioinformatics methods of the last 20 years, combined for both speed and accuracy.
Run analyses through the web interface, or integrate Fathom directly into your pipeline with the API.
Upload reads, choose a reference, and view interactive composition and pathogen results. No setup, no command line.
Submit samples and pull results programmatically. Drop Fathom straight into your existing sequencing workflow. Every call the app makes is available to you, with a sign-in token.
Fathom does not save your sequencing data long term. We respect your privacy and don't retain your data to monetize it, unlike most other platforms. Fathom takes security seriously and is secure by design, built on industry-standard patterns.
Questions about an analysis, or a project that needs more than the platform offers? We read every message.
Help with your account, uploads, or interpreting a result. Email us and include the sample accession if it concerns a specific analysis.
support@fathom-genomics.comBusiness needs, volume pricing, and consulting services, including custom references, bespoke pipelines, or analysis of your data by our team.
sales@fathom-genomics.com