Basic bioinformatics pipeline in bash and Nextflow for Local use.
Scripts inlude:
BWA_GATK.sh: A bash scripts downloads a paired-end file from SRA, aligns the reads to genome using BWA and calls SNPs using GATK.
GATK_Nextflow.sh: Nextflow adaptation of BWA_GATK.sh
Nanopore_Variants: A basic bash script to call variants from FAST5 file of Oxford Nanopore Technologies Sequencing Platform.