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Release 1.1.0
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@DennisSchmitz DennisSchmitz released this 15 Sep 12:54
· 124 commits to master since this release
v1.1.0
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Release of Jovian version 1.1.0

⚠️ important notice: if you're upgrading from 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

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