The main steps, software, and code/parameters used from off-machine data to the VCF file in whole-genome sequencing data analysis.

A fully automated and reproducible Whole Genome Sequencing (WGS) pipeline built with Snakemake. Implements GATK Best Practices for alignment (BWA), variant calling, and functional annotation (SnpEff) on human (GRCh38) data.

CNV Analysis Next-gen Variant Assessment Suite

A comprehensive pipeline for detecting, characterizing, and visualizing recombinant AAV (rAAV) integration sites using Oxford Nanopore long-read sequencing data.

T2T (UCSC hs1) mapping pipeline for human WGS (SRA) using SGE + Singularity. Originally built for schizophrenia neuron TE analysis.

HBV whole-genome sequencing pipeline for Oxford Nanopore data

sppComp describes species composition of Saccharomyces samples and allows the raw detection of genomics signatures such as inrogressions, CNVs and aneuploiudies

Xtreme Archaeal Analysis (X-ARCH) is a bioinformatics pipeline for the assembly, binning, and metabolic characterization of Archaeal Metagenome-Assembled Genomes (MAGs) from extreme environments. Includes automated QC, taxonomy (GTDB-Tk), functional annotation (DRAM/antiSMASH), and NCBI submission formatting.

Workflow and scripts related to WGS analysis

Pipeline designed to evalute FFPE processing kits through qc, variant calling, and truth set comparison analysis. Configured for AWS Batch deployment.

Code, data, and results for the phylogenetic resistance manuscript

Comprehensive WGS variant analysis of Pseudomonas aeruginosa (SRR34663677) — includes quality control, alignment (BWA-MEM), variant calling (GATK), annotation (SnpEff), and AMR interpretation.

software for processing tuberculosis whole genome data. interface to the BWA, VarScan, SamTools etc.

Contain projects in bioinformatics fields

🤖 Enhance coding with Plato, a CLI-compatible AI assistant that streamlines coding tasks while integrating seamlessly with GitHub Copilot.

NGS Processing Pipelines for WGS and WES data

Curated lists of features for Mtb genomic analysis

🧬🔍CNV analysis and outcome prediction in Ultra-High-Risk and First Episode Psychosis individuals 🩺🧠