🧬 Genomics & Public Health Bioinformatics

• NGS Workflow Development
  ▸ End-to-end pipelines for Illumina & Nanopore data
  ▸ De novo genome assembly, polishing, and annotation
  ▸ Reference-based mapping, variant calling, consensus building
  ▸ Quality control and contamination detection
  
  

• AMR Surveillance & Genomic Epidemiology
  ▸ AMR gene prediction: AMRFinderPlus, ResFinder, CARD
  ▸ Phylogenetic reconstruction: IQ-TREE, RAxML, FastTree
  ▸ Transmission mapping: Microreact, Nextstrain, GrapeTree
  ▸ Metadata integration: iTOL, Pathogenwatch, ExcelR, R/tidyverse
  ▸ Genomic clustering and outbreak detection
  
  

• Metagenomics & Microbiome Analysis

▸ Taxonomic classification: Kraken2, Bracken, Centrifuge, Kaiju

▸ Resistome and virulome profiling: RGI, AbritaMR, resfinder

▸ 16S/ITS pipelines: DADA2, QIIME2

▸ Environmental and wastewater metagenomics

▸ Visualization: Krona, Pavian, phyloseq, ggplot2

💻 Programming & Scripting

• Languages:
  Python, R, Bash, SQL, HTML, YAML
  
  

• Packages & Libraries:
  ▸ R: tidyverse, tidymoels, Bioconductor, phyloseq, ape, caret, ggplot2
  ▸ Python: pandas, Biopython, matplotlib, seaborn, scikit-learn
  ▸ Workflow control: Snakemake, Nextflow, Makefiles
  ▸ Reproducible analysis: Quarto, RMarkdown, JupyterLab
  
  

• Version Control & Documentation:
  Git, GitHub

⚙️ Workflow Automation & Data Reproducibility

• Workflow Managers: Snakemake, Nextflow

• Containerization: Singularity, Docker

• Computing Environments: Linux (Ubuntu), HPC clusters (SLURM)

• Reproducible Reporting: Quarto, RMarkdown, JupyterLab, GitHub, VSCode

🧬 Pathogen Genomics & NGS Analysis

• Data Processing: fastp, FastQC, multiQC, seqtk, BBMap
  
  

• Genome Assembly & Annotation: SPAdes, Unicycler, QUAST, Prokka, PGAP, Busco, CheckM
  
  

• Variant Analysis: BWA, Bowtie2, samtools, bcftools, iVar, LoFreq, FreeBayes, GATK
  
  

• Consensus & Coverage: BEDtools, mosdepth, ivar consensus, seqkit stats
  
  

• AMR & Gene Profiling: abricate, AMRFinderPlus, CARD, ResFinder, RGI, PointFinder
  
  

• Typing & MLST: MLST, chewBBACA, cgMLST, SISTR, Kleborate, TB-Profiler
  
  

• Phylogenomics & Clustering: Nextstrain, IQ-TREE, RAxML, Mash, SNP-dists, Microreact 

🧬 Pathogen & AMR Surveillance Tools

• Data QC & Preprocessing: fastp, FastQC, multiQC, seqkit, Trimmomatic, nanoQC porechop, nanoFilt
  
  

• Assembly & Annotation: SPAdes, Flye, megahit,  Unicycler, QUAST, CheckM, CheckV, Busco, Prokka, PGAP
  
  

• Variant Calling: BWA, Bowtie2, samtools, iVar, LoFreq, bcftools, GATK, FreeBayes
  
  

• Consensus Generation & Coverage: iVar, BEDtools, mosdepth, Qualimap, seqtk
  
  

• AMR Profiling: abricate,  AbritAMR, AMRFinderPlus, CARD, ResFinder, RGI, PointFinder
  
  

• Typing & Genotyping: MLST, chewBBACA, cgMLST, Kleborate, TB-Profiler, SISTR
  
  

• Functional Annotation: HUMAnN, eggNOG-mapper, Metaxa2, fmh-funprofiler, Dada2
  
  

• Microbiome Stats: phyloseq, vegan, microbiomeSeq, DESeq2, ALDEx2

• Taxonomic Classification: Kraken2, KrakenUniq, Centrifuge, Kaiju, Bracken, MetaPhlAn

🧪 Phylogenomics, Clustering & Epidemiology

• Phylogenetics: IQ-TREE, RAxML, FastTree, MAFFT, SNP-sites, SNP-dists, parsnps
  
  

• Genomic Epidemiology Platforms: Nextstrain, Augur, Microreact, Phandango, PopPUNK
  
  

• Lineage Assignment: pangolin, Nextclade, GrapeTree, SNPcluster

Familiarity with Sequencing & Multi-Omics Data Types 

• Whole Genome Sequencing (WGS)

• Illumina Paired-End Reads

• Oxford Nanopore Technologies (ONT) Long Reads

• PacBio HiFi Long Reads

• Hi-C Chromatin Conformation Data

• 16S and 18S rRNA Amplicon Sequencing

• Shotgun Metagenomics

• Hybrid Assemblies (e.g., Illumina + ONT / PacBio)

• RNA-Seq / Transcriptomics

• Environmental DNA (eDNA)

• Targeted Enrichment Panels (e.g., ARTIC, VSP2)