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panaroo

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IbrahimElzahaby / Erasmus_MC_Internship

Plasmidome analysis to track the transfer route of AMR genes in bacteria

fasta-sequences rgi antimicrobial-resistance-genes prokka plasmidfinder abricate virulence-genes antimicrobial-genes-annotation amr-detection refseq-genbank panaroo

Updated Oct 15, 2023
Jupyter Notebook

Savagebd / comparative-bacterial-genomics-pipeline

Reusable comparative bacterial genomics pipeline for assembled bacterial genome FASTA files using QUAST, Bakta, FastANI, Panaroo, and FastTree.

bioinformatics comparative-genomics phylogeny quast fastani panaroo bacterial-genomics bakta genomics-pipeline

Updated May 27, 2026
Python

gmboowa / rMAP-GWAS

Portable WDL/Cromwell workflow for microbial case-control GWAS from paired-end reads, producing annotated pyseer associations & HTML reports.

bioinformatics cromwell pathogen-genomics wdl-workflow genomic-surveillance panaroo pyseer microbial-gwas unitig-caller

Updated Jun 17, 2026
WDL

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