Control-FREEC based CNV calling pipeline for preimplantation genetic testing (PGT-A) and aneuploidy detection using panel-of-normals approach

WisecondorX-based NIPT pipeline for fetal CNV prediction, aneuploidy screening, and panel-of-normals reference construction

KrakenUniq-based metagenomics screening pipeline for microbial classification of human-derived NGS data with Excel report generation

Targeted virome capture panel design pipeline for hybrid-capture NGS enrichment of vertebrate DNA and RNA viruses from clinical and environmental samples

Modular shell pipeline for adapter trimming, genome alignment to GRCh38, and chromosome-level read mappability profiling using Bowtie2 and SAMtools

Modular FASTQ preprocessing pipeline for quality control (FastQC/MultiQC) and adapter trimming (Cutadapt/Trimmomatic) of NGS sequencing data

Modified ichorCNA to estimate fetal fraction of cell-free DNA from ultra-low-pass sequencing (ULP-targeted-seq, 0.1x coverage).

Germline variant calling pipeline using FastQC, BWA, GATK HaplotypeCaller, VEP and ANNOVAR for paired-end NGS data

5-Day Gen AI Intensive

End-to-end somatic and germline variant calling pipeline using BWA, GATK HaplotypeCaller, VEP and ANNOVAR for tumor NGS analysis

GSEA-based transcriptomic analysis of COVID-19 impact on blood-brain barrier gene expression using GEO datasets (GSE167000, GSE179923)

First Git Repo

LetsUpgrade Python program