A new version of RAMPART, our software for analyzing nanopore data in real-time, is now available. This brings a number of major changes which should help with SARS-CoV-2 analyses. There are no changes to how RAMPART is run.
v1.1.0 major changes
- Guppy-demuxed FASTQs can now be used. If this is the case, then
porechopis no longer a requirement for RAMPART to run.
- The memory footprint has been drastically reduced. Testing with 1 million SARS-CoV-2 reads results in only ~20Mb for the server and ~10Mb for the client. Achieving this necessitated the removal of filtering & the ability to change barcode-sample names via the UI. We hope to bring back this functionality in a future release.
- Bugs in the “Export Reads” pipeline should now be fixed.
- Improved installation documentation
v1.1.0 minor changes:
- FASTQs can now be in nested folders (currently 2 levels are allowed)
- Light and Dark themes are now available and may be changed via a toggle in the header.
- We now display the version number in the footer to help with bug reports & debugging.
- Various other minor bugfixes and improvements.
If there are any bugs or feature requests, please make an issue in the RAMPART GitHub repo and we’ll try to improve things. If you are able to contribute to development your help would be extremely welcome.
How to install
artic-ncov2019 conda environment, you can install via:
conda install -y artic-network::rampart==1.1.0
If there are any issues, you may reinstall the version of RAMPART which came before this via
conda install -y artic-network::rampart=1.0.
Please see the installation docs for further help, including how to install from source or into new conda environments.
More frequent future releases
We hope to release further rampart versions over the coming weeks specifically targeted at improving our ability to sequence SARS-CoV-2. We’ll do this via publishing “release candidate” versions to conda and crowd-sourcing testing via those who are able and willing! Official releases will then be announced here, and we’ll also update the ncov19 repo.
Keep up the good work everyone,
James Hadfield // ARTIC network