Lead Bioinformatician

Developed Snakemake pipelines for variant calling, variant annotation, RNA-Seq, and neoantigen identification analysis. Developed Nextflow pipelines for somatic and germline variant identification, designed for manual and automated operation via the Seqera Tower platform. Migrated bulk RNA-Seq analysis workflows from R scripts to Nextflow, improving scalability. Developed a fully functional BASH pipeline for variant identification and annotation, deployed on AWS EC2 instances with storage in AWS S3 bucket. Conducted RNA-Seq analysis for multiple tissue samples on the Seven Bridges platform. Developed a pipeline using BASH and R Bioconductor to perform single cell classification and annotation based on marker-specific expression. Utilized long-read assembly tools, such as Flye and Canu, and polishing tools like Racon and evaluation of long-read genome assemblies using QUAST.