Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

vSNP -- validate SNPs

A nextflow pipeline for polishing CLR assemblies

vSNP -- validate SNPs

a better freebayes-parallel

This directory contains material that I've used in different courses

A workflow for using SpeedSeq to align and call SVs from WGS data

Codes for exome sequencing class being taught by Tychele N. Turner, Ph.D.

Short read mapping and variant calling

mtb-mixed-infection-pipeline enables detection of mixed Mycobacterium tuberculosis infections using a reproducible workflow that integrates Snippy, FreeBayes (pooled mode) & MixInfect2. It processes raw reads through alignment, variant calling & statistical analysis to identify mixed-strain infections

BSA-QTL Mapping in Drosophila Ananassae

Multi-class classification of drug resistance in MTB clinical isolates

Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control

Multi-class classification of drug resistance in MTB clinical isolates

Nextflow resequencing pipeline with bwa-mem and freebayes