Bioinformatics on GCP, AWS or Azure

Official code repository for GATK versions 4 and up

sysadmin tasks made easier

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

High performance data storage for importing, querying and transforming variants.

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

Learning the Variant Call Format

Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.

GitHub for the SIB courses NGS - Genome variant analysis

Nextflow implementation of the GATK HaplotypeCaller pipeline

Whole Exome/Whole Genome Sequencing alignment pipeline

Workflows for whole-genome/exome sequencing data analysis

This repository contains data and code for our analysis of the genome of a Plasmodium falciparum strain with reduced susceptibility to Artemisinin-Based Combination Therapy (ACT) drugs. We performed whole-genome sequencing of the HSOG3 clinical isolate and compared it with a large dataset of global P. falciparum samples.

Some workflows I wrote for my phd projects

GATK WGS workflow

This Snakemake pipeline implements the GATK best-practices workflow

Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.

Bash scripts for fastq to vcf pipeline, written for USyd Artemis HPC.