v1.1.0

• Host Filtering : STAR (v2.7.3) vs GRCh38
• Preprocessing : Trimmomatic (v0.39, TruSeq3-PE-2 adapters)
• Taxonomic Profiling : Kraken2 (v2.17.1)
  • Database : PlusPFP (k2_pluspfp_20260626)
  • Confidence Score : 0.2
  • Flag : --report-minimizer-data (Unique minimizers extraction)
• Decontamination : Dynamic ROC / Youden J-index calibration via multi-organ cohorts & BacDive habitat annotation (DSMZ)
• License : CC BY-NC 4.0

V1.0.2-beta

• version modified by remy and lucie
• DNA 16S scripts added

Ali Youncha internship

First version of the microbiote pipeline

V1.0.1 - Ali internship last version

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