Release 1.1.0
Release of Jovian version 1.1.0
Jovian 1.0.x
to Jovian 1.1.0
then please execute bash jovian --update
twice
This release includes the following changes and improvements:
General improvements:
- The Jovian workflow(s) have had a significant make-over, improving speed, structure, and code-readability.
As an added bonus: all workflow(s) now follow the same code style and structure for improved clarity - All python code now follows the same formatting
- "Redesigned" various functions within Jovian for improved speed and user-feedback
- Various stability changes to the "Jovian_master" and "Jovian_helper" environments
- Fixed a bug in the Jupyter notebooks configuration
- Fixed several bugs in the database installer
- Improvements have been made to the database installation process
- The Notebook Report should now display all your run information automatically.
Introducing multiple workflows in Jovian
Jovian used to be exclusively a viromics/metagenomics workflow. However, Jovian now supports multiple workflows that the user can choose to execute.
You're able to choose from the following workflows:
- Illumina Metagenomics
- Illumina Reference alignment (new 🎉)
- Nanopore Reference alignment (new 🎉)
Illumina reference alignment:
- Improved consensus calling, added indel calling.
- Visualized minority SNPs in
IGVjs
for manual inspection. - Fixed a bug with the rendering of the GC-content track in
IGVjs
. - Fixed a bug, human data is now correctly removed.
- When new majority SNPs are found after the consensus sequence is generated, a warning is thrown. Manually assess the alignment in
IGVjs
and determine if a another round of alignment is required. This is a work in progress. - Code cleanup, work in progress.
- Importantly, please double check the consensus genomes generated with coverage low coverage (<10x) manually in the provided IGVjs viewer to assess errors: mistakes are observed at these coverages.
Nanopore reference alignment:
A new workflow designed for processing and aligning Nanopore (multiplex pcr sequencing) data to a reference.
- Removes adapter sequences
- Removes overrepresented primer sequences
- Removes background host information (human genome)
- Performs Quality Control specific for nanopore data
- Aligns the data to a user-given fasta
- Creates a consensus genome with various depth-of-coverage thresholds [1x, 5x, 10x, 30x, 100x]
- Produces information about the "Breadth-of-coverage" (percentage of the reference which could be aligned) for each coverage threshold
- Detects majority SNPs and displays this information in an easy-to-read table
Documentation of Jovian can now be found on jovian.rivm-bioinformatics.com