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Primary Analysis - Base calling, quality scoring, adapter/low-quality trimming, demultiplexing
Secondary Analysis - Alignment (mapping) reads to a reference genome, variant calling (identifying differences like SNPs, indels)
Tertiary Analysis - Annotation, Filtering & Prioritization, Interpretation, Visualization & Reporting
Tools Experience
BLAST
Conda/Mamba
Docker
Galaxy
R/Bioconductor
Python
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Bowtie
Bedtools
NCBI Databases
UniProt
PSIPRED / PDB / PyMol
MEGA / MrBayes / CIPRES
Clustal Omega/MAFFT/T-Coffee
UCSC Genome Browser / Ensembl
scikit-learn / TensorFlow / Keras
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