Natrix2 v2.0.1

Natrix2 v2.0.1 - Release

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Changelog

[2026-01-01]

• Update README structure and content
• Update CHANGELOG
• Bump MultiQC to v1.33 and fix Conda environment issue
• Refine filter_unclassified.py unclassified handling
• Apply filter_unclassified to Illumina Mothur outputs
• Fix logical operator in classify.smk rule for vsearch
• Reorder channels in natrix.yaml
• Fix Mothur _unclassified taxonomy repetition
• Release Natrix2 v2.0.1

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[2025-12-03]

• Rewrite merge_mumu_output_2.py with new merge-key logic
• Add handling of empty/missing mumu OTUs
• Preserve all BLAST OTUs (right-join)
• Generate new OTU identifiers from merge key and size
• Add unmerged_seqids.csv output
• Standardize outputs to use seqid as index label
• Clean up script and update Snakemake rule

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[2025-11-17]

• Fix download issue of the NCBI database for BLAST
• Add packages to blast.yaml
• Update BLAST version in blast.yaml
• Remove the screen package from natrix.yaml
• Update and revise CHANGELOG.md

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[2025-10-12]

• Update README.md and revise the Troubleshooting section

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[2025-09-26]

• Add new section "Common issues" to README
  • Add "Causes of pipeline aborts"
  • Add "Problems with installation"
• Update .gitignore

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[2025-07-14]

• Update text color in filename.png to improve readability
• Add citation section to README.md
• Add CITATION.cff file for GitHub citation support

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[2025-06-13]

• Update README.md with the latest usage instructions and options
• Update docker_manual.tex and docker_manual.pdf

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[2025-06-12]

• Add output file multi_hits_blast_mumu.csv to log all duplicate OTUs
• Allow no_filter as a valid option for drop_tax_classes in the config file
• Update merge script merge_mumu_output_2.py:
  • Retain only duplicate entries with pident ≥ 90
  • Select the best hit per OTU based on highest pident
  • Export all duplicates to multi_hits_blast_mumu.csv for traceability
• Update all pre-set config files
• Update README.md with the latest usage instructions and options
• Improve image backgrounds for better visual clarity