ChroQueTas v1.0.0

Release ChroQueTas v1.0.0 with new improvements as described in the publication that is out today in Nature Microbiology: https://www.nature.com/articles/s41564-025-02084-7

v0.6.0-Zenodo

Minor changes for Zenodo release. Repository containing ChroQueTas code as well as instructions to recreate Figure 6 from Nature Microbiology 2025 publication

ChroQueTas v0.6.0

Novel release of the tools with updates:

• Increased FungAMR database with 57 species, 210 proteins and a total of 8,285 mutations associated with AMR (more info can be extracted by using --list_species flag
• Included novel function from miniprot that allows choosing the genetic code for translation. The genetic code can be manually selected by the user and the -c/--trans_code flag. By default, the genetic code is automatically set by ChroQueTas according to the -s/--species flag (formerly --scheme, but renamed to avoid confusion, issue #3) , so it would be set to "alternative yeast code" (-c 12) for the species within the CTG clade or to the "standard code" (-c 1) for the other species. You can inspect the default behavior here
• Reporting of AMR based on the degree of evidence per mutation, as described in the preprint.
• Extended outputs as described here
• Additional minor updates for improved performance

ChroQueTas v0.4.2

Minor changes in the main pipeline. Fixed bugs reporting issues when highly-fragmented genomes are investigated

ChroQueTas v0.3.3

Minor changes in the main pipeline, replacing how ChroQueTas finds mutations by "FungAMR mutation".
The mutations must be checked with the FungAMR database in order to infer their level of evidence, as not all level of evidence represent AMR by their own.

ChroQueTas v0.3.2

This release correspond to the version of the software used for the analysis of 46 C. albicans and 144 Z. tritici genomes as described in the preprint of the publication: https://www.biorxiv.org/content/10.1101/2024.10.07.617009v1