Fastqc: check if the input fastq file(s) are sanger/illumina 1.9 encoding fastq groomer: reformat fastq file(s) to sanger/illumina 1.9 encoding if necessary fastq trimmer or trimmomatic: remove low quality regions alignment (e. g. bowtie2/bwa/hisat): align reads to a reference genome, giving bam/sam files sam-to-bam: convert the output file(s) to bam files if the output from the last step is a sam file variant calling (e. g. freebayes): call variants using output bam file and reference genome, giving vcf file