https://github.com/cbg-ethz/cojac - Version 0.9.3 - tables for LolliPop

preview feature:

• produce tables that can be used for LolliPop

  • tabmut: --add-mutations — add mutations strings to tabmut

  Necessary for using "bootstrapping" confidence intervals in LolliPop - cooc-mutbamscan: --fix-subsets — subset of coocurring mutations

  Fix variants attribution when cooccurrence are subset/superset of other variants: if var 1 has mutations A, B and C and var 2 has mutations A and B amplicon with mutations A and B is flagged to both var 1 and 2

  Useful for, e.g., delta and early omicron waves.

- Jupyter Notebook
Published by DrYak over 1 year ago

https://github.com/cbg-ethz/cojac - Version 0.9.2 - LAPIS improvement

Bugfixes and improvement for sig generation from GeneSpectrum:

• support LAPIS v2
• switch to lineage field
• quirk field to workaround bugs in servers

Preview feature:

• alpha importer from NextStrain

- Jupyter Notebook
Published by DrYak almost 2 years ago

https://github.com/cbg-ethz/cojac - Version 0.9.1

Bug fixes: - --url was broken in sig-generate and cooc-curate

New features: - sort BED file by position, on by default (avoids wrong amplicons names in out-of-order file) - comment amplicons query file, on by default (add comments such as # SARS-CoV-2_25_RIGHT) - helps double check amplicon names - simplify searching for primers affected by mutation by (ab)using COJAC's cooc-mutbamscan and primer BED files

- Jupyter Notebook
Published by DrYak over 2 years ago

https://github.com/cbg-ethz/cojac - Version 0.9

• Converted to a proper python package with poewtry and click
  • Command format has changed
• Integrated into V-pipe
• Tool for generating list of mutations from Cov-Spectrum to be used in creating COJAC's specific YAML files
• Select API end-point on Cov-Spectrum (ENA or GISAID)
• Accesskey for non-open (GISAID) on Cov-Spectrum
• Tool for converting list of mutations from TSV on Covariants.org repo
• Partial support for aarch64
  • pysam still missing on bioconda

Publication: - change of literature ref to Nature Microbiology - Notebooks used in publication more portable

- Jupyter Notebook
Published by DrYak about 3 years ago