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

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

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

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

Short read mapping and variant calling

Reproducible Galaxy-based diagnostic-style WES analysis of public SRA samples focused on CVID/IEI-associated genes.

Multi-class classification of drug resistance in MTB clinical isolates

BSA-QTL Mapping in Drosophila Ananassae

Automated Bash pipeline for variant analysis in family trio. From raw FASTQ to VCFs. Supports Mendelian inheritance models (AR, de novo, AD) using Bowtie2, FreeBayes, Bedtools and BCFtools. Includes integrated QC reports (FastQC, Qualimap, MultiQC).

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

Multi-class classification of drug resistance in MTB clinical isolates

Reproducible variant calling pipeline using Snakemake, processing real NGS data from raw FASTQ files to final VCF output with QC, alignment, and variant detection.

Nextflow resequencing pipeline with bwa-mem and freebayes

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