New release 3.0.1 - 2025/01/02

What's Changed

• bump 3.0.1 version by @saramonzon in #24

Full Changelog: 3.0.0...3.0.1

New release 3.0.0 - 2025/01/02

• Code refactor to create a proper python package
• Implementation of parallel computation for execution speed.
• New implementation of reference-alleles module using leiden algorithm for allele clustering.
• New param defaults based on empirical testing.
• Distance matrix is rewritten with more params available.

What's Changed

• Merge tag '2.0.1' into develop by @saramonzon in #10
• Refactorization of Analyze schema by @luissian in #11
• Implemented changes described in comments in the previous PR by @luissian in #13
• Feature/reference alleles by @luissian in #14
• Fixing issue for reference allele by @luissian in #15
• fixed issue too many open files by @luissian in #16
• Enhancements reference alleles processes by @saramonzon in #18
• Feature/allele calling by @luissian in #17
• Implemented distance matrix by @luissian in #20
• Fixes in allele calling module by @saramonzon in #21
• Fixes and enhancements by @saramonzon in #22
• Release 3.0.0 by @saramonzon in #23

New Contributors

• @luissian made their first contribution in #11

Full Changelog: 2.0.1...3.0.0

New release 2.0.1 !

New features

• New default missing values threshold imposed for samples in distance matrix creation
• New default perc_identity_ref value for loci search in allele calling analysis
• Github actions for testing and docker generation.

Bug fixes

• multiple statistic modes bug fixed
• BLAST database creation bug due to punctuation signs in file name fixed
• ST profile identification bug fixed
• Python modules installed from conda-forge in environment.yml

Documentation

• Channel order in conda installation command

New release 2.0.0!!

New features:

Bug fixes:

Taranis beta release 0.3.3 05-Nov-2018

Fix num_threads in blast commands

Taranis beta release 0.3.2 02-Nov-2018

BUG FIX:

• Added ERROR posibility to allele classification, when the allele is not PLOT but is too near to contig end, and protein codification finishes without finding a stop codon.

Taranis beta release 0.3.1 27-Oct-2018

• Added cpus as parameter.

Taranis beta release 0.3.0 25-Oct-2018

Bug fixes:

• Allow dependency check for versions greater than needed.

Features:

• Added graphics for schema evaluation(beta)
• Added SNP calling (beta)

Taranis beta version

• cg/wgMLST analysis using assembled contigs as input using a defined schema. Comparison matrix is generated for phyloviz visualization. Blast hit are classified as Exact match , new allele, etc.
• cg/wgMLST statistics.
• beta: SNP analysis.
• Insertions, deletions and paralogues detection.