Meteor 2.0.22

✨ New Features

Enhanced Strain Analysis Metrics (#70)

• Pairwise comparison of strains
• Information content classification (minimal vs. maximal information sites)
• Automated strain relationship categorization based on genetic distance thresholds

🐛 Bug Fixes & Performance

Threading Stability Improvements

• Updated cogent3 and bzip2 dependencies to resolve multi-threading issues
• Enhanced parallel processing reliability for high-throughput workflows

🗄️ Database Updates

KEGG Modules v116

• Updated to KEGG Release 116 by @fthirion89 (#115)
• Latest metabolic pathway annotations for improved functional classification

🛠️ Developer Experience

Repository Configuration

• Added .gitattributes by @fplazaonate (#117)
• Improved language detection and diff handling for binary files

Full Changelog: 2.0.21...2.0.22

Meteor 2.0.21

Bug Fixes

• Fixed incorrect link to human oral catalogue
• Fix duplicate annotation for resfinder

Improvements

• Improved strain analysis performance
• Implemented ultrametric distance calculations for strain analysis
• Added Python 3.13 compatibility updates

Full Changelog: 2.0.20...2.0.21

Meteor 2.0.20

Bug Fixes

• Fixed strain analysis: Resolved issue where a bed file was incorrectly required as input
• Fixed reference date warning related to catalogue date validation

Enhancements

Updated catalogue annotations:

• Upgraded to GTDB r226 taxonomic annotation
• Updated to dbCAN 5.0 for enhanced carbohydrate-active enzyme annotation

Added Nextflow pipeline template: Introduced nf-meteor.nf workflow for automated end-to-end analysis with simplified parameter configuration.

Meteor 2.0.19

Main improvements:

• Fix compatibility with nextflow
• Fix strain issues with sort
• Update Kegg modules to 114

What's Changed

• Make json files human readable by @fplazaonate in #79
• Improve counter by @fplazaonate in #83
• Remove unnecessary else statements after for loops by @fplazaonate in #86
• Improve counter by @fplazaonate in #87
• Improve tests for counter by checking the entire contents of dictionnaries. by @fplazaonate in #88
• Compute gene abundance in total and unique modes without pysam by @fplazaonate in #89
• Fix wrong counted_reads in total counting mode by @fplazaonate in #90
• Improve counter by @fplazaonate in #91
• Fix permissions bug with a single vcf file by @fplazaonate in #92
• Add bcftools sort step by @aghozlane in #101
• Improve CLI parser by @fplazaonate in #102
• Update KEGG module definition to v114 by @fthirion89 in #105
• Close Issue #85 and Issue #95 by @fthirion89 in #106
• Improve json (Issue #97) by @fthirion89 in #110
• Issue #108: Add mapping rate after counting by @fthirion89 in #109
• Update profiler.py by @fthirion89 in #107
• Strain issues by @aghozlane in #111

Full Changelog: 2.0.18...2.0.19

Meteor 2.0.18

New Features:

• Enhanced Meteor Interaction: Improved testing of entries ensures a more robust and reliable interaction with Meteor.
• KEGG Modules Analysis: Meteor now provides insightful analysis of KEGG modules, offering a deeper understanding of metabolic pathways.
• Optimized Strain Analysis: Our strain analysis parameters have been fine-tuned for more accurate and efficient results.
• Faster Tree Computation: The TN69 metrics are now available for tree computation, significantly reducing processing time compared to GTR.
• Catalogue Version Checking: Meteor now verifies that the catalogue version is compatible with the current Meteor version, ensuring seamless integration.

Bug Fixes:
This release also includes multiple bug fixes, improving stability and performance across different functionalities.

Meteor 2.0.17

New Features:

• Builder: The reference is now compressed using bgzip, consistent with our catalog listings. This enhancement ensures efficient storage and compatibility across tools.
• Catalogues: We have standardized the annotation format and enhanced usage with the Feather format. Additionally, the Resfinder and ResfinderFG databases are now fully integrated and available for use.
• Mapping: Meteor now provides more detailed and informative outputs regarding the counts, offering users better insights into the mapping process.
• Strain Analysis: Our strain analysis parameters have been further optimized, and multiprocessing has been enabled for enhanced performance and faster analysis.
• Tree Computation: Multiprocessing support is now active, allowing for quicker and more efficient tree computations.

Bug Fixes:
This release also includes multiple bug fixes, improving stability and performance across different functionalities.

Meteor 2.0.16

We have improved the stability of the strain analysis.

Meteor 2.0.15

We have completely revised the strain analysis. Meteor is now based on freebayes.
Several dependencies have been removed: raxml and bcftools.

2.0.14

What's Changed

• Fix tree path list by @fthirion89 in #50

New Contributors

• @fthirion89 made their first contribution in #50

Full Changelog: 2.0.13...2.0.14

Meteor 2.0.13

• Fix strain analysis for some catalogues
• Enhanced Mutation Rate Analysis
• Extend testing coverage
• Solving Malfunctioning Strains with some microbial catalogs
• Activate GBM analysis
• Introducing automode for Rapid and Normal Analysis
• Tests covers 92% of the code