Release v0.7.0

Changes

• Maker a separate CLI operation for the computation of the cooccurrence matrix --covigator-cooccurrence-matrix. Optimizes the previous implementation. Adds support for GISAID. Adds a filter of mutations by length in order to optionally remove very long indels.

Release v0.6.6

Changes

• Add DB patch for mismatching domains between pipeline and database
• Ensure order of callbacks in recurrent mutations tab + some other corner cases
• Avoid lineages from pangolin with the string "None"

Relase v0.6.4

Changes

• Added an option to skip VCF loading in DB. This is useful to reload sample metadata into the database without needing to reload all VCFs. To use this mode use the environment variable COVIGATOR_SKIP_VCF_LOADING=true

Release v0.6.2

Changes

• Fix issue with repeated months in a dropdown
• Remove LRU caches that were causing trouble more than helping
• Fix import script

Release v0.6.1

Changes

• Add a link to documentation in contextual menu
• Update the documentation for the pipeline and the knowledge base
• Change logos

Release v0.6.0

Changes

• Upgrade to CoVigator pipeline v0.9.3 (https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/releases/tag/v0.9.3) from v0.7.0 provides:
  • Phasing of clonal mutations. Mutations affecting the same amino acid are now reported together in a MNV and its effect its correctly calculated
  • Run pangolin to determine SARS-CoV-2 lineages
  • Variant allele frequencies are now computed with vafator https://github.com/TRON-Bioinformatics/vafator
• Integrate pangolin data and add its own tab
• Reorganise tabs
• Add counter for samples, oldest and most recent sample
• Separate tables for ENA and GISAID
• Separate low frequency mutations into its own table
• Implement a sequential downloader for ENA FASTQs as distributed downloader was causing trouble when scaling out

Release v0.5.1

Changes

• Style improvements
• Added a navigation menu
• Added information of last update of each dataset
• Better resolution logos

Release v0.5.0

Changes:

• Cleaner separation of ENA and GISAID with two different URLs and different sets of tabs

Release v0.4.3

Changes:

• Replace about tab by acknowledgements tab

Release v0.4.1

Minor changes

• Remove some outdated reference to GISAID data in the downloads tab
• Make links in help tab to open in a different tab

Bugifx

• Wrong count of countries
• Fix plotly version to avoid issue on line plot