COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource

public sequences ready for download!

May 2021 update: we are now at 86,377 sequences with normalized metadata on AWS OpenData!

Edit text!



COVID-19 PubSeq is run by a community of bioinformaticians and software developers working at leading institutes (see sponsors below) with the goal of making online analysis available to everyone. You can talk with us directly in the matrix PubSeq room. We are open to improving tools, work flows and analysis.

1.1 Oxford Nanopore Analysis

We run Oxford Nanopore ourselves. It is an exciting technology because it gives us an accurate SARS-CoV-2 sequencer for a few thousand dollars which can be run in a living room! With PubSeq we aim to make it easy to analyse Nanopore material using our free Cloud infrastructure and the NVIDIA Jetson computer. If you need help in using the online workflows don't hesitate to contact us.

1.2 Data from other sequencers

We accept FASTA sequences of SARS-CoV-2. Simply upload them using the web form and/or REST API. No sign-up required! If you have large scale short read data and require support we can discuss that. We also run Illumina sequencing in several places.

1.3 Professional support

To use COVID-19 PubSeq solutions for professional purposes you can contact Boston based Curii, the creators of Arvados, directly.

COVID-19 is built on Arvados using CWL workflows.

1.4 E-mail

For questions feel free to write directly to Pjotr Prins.

Edit text!