Read alignment is a common process applied to high-throughput sequencing data, being one of the first stages required for many different types of analysis. In the DNA-Seq scenario, this process is applied for variant calling and before the polishing procedure. The goal of the read alignment is to map short sequencing reads efficiently to a large reference genome to identify the 'correct' genomic loci from which the read originated whilst taking into account errors in the sequence reads.
This functionality can be found under Genome Analysis → DNA-Seq Alignment.
Two alignment strategies are available:
BWA: BWA is a software package for mapping log-divergent sequences against a large reference genome. The BWA-MEM algorithm, which is used, is a good choice for high-quality and accurate DNA-Seq alignments.
Bowtie 2: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning read of about 50 up to 100 nucleotides.