snakemake-illumina-gatkvariant

A Snakemake workflow for variant calling using GATK4 best practices

AlleleFreqPipe

An R script for generating allele frequencies from DNA/amino acid sequence alignments.

snakemake-illumina-fastqc

A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC

PlasmoSeq-DualTech

A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries