Genome alignment tools: BWA-MEM or DRAGMAP?

Monika Opalek, PhD

April 28, 2023

Alignment involves the step when the short fragments of DNA sequence are being matched to the reference genome. For the workflows available on the IntelliseqFlow platform, we offer a choice of two alignment tools: BWA-MEM or DRAGMAP. While both tools are designed to perform the same task, they differ in their underlying algorithms and performance characteristics.

Both BWA-MEM and DRAGMAP are widely used and are efficient, accurate tools for genome alignment. BWA-MEM is the most popular tool for genome alignment, is used in a variety of pipelines and software packages, and has been cited tens of thousands of times in research articles [1, 2]. BWA-MEM has been also used in many large-scale projects such as the 1000 Genomes Project [3] and the Human Genome Project [4]. It uses a seed-to-extend approach where sequences are first cut into short fragments (seeds), aligned to reference, and then extended in both directions from a seed to create the final alignment. Its speed and accuracy make it an ideal choice for analysing large datasets  most commonly when multiple whole-genome sequencing datasets are involved.

In contrast, DRAGMAP was developed by the Genome Informatics Section at the National Human Genome Research Institute (NHGRI) [5]. It uses a divide-and-conquer approach where the reference sequence is divided into small overlapping regions (tiles), and the input sequences are then aligned to the reference simultaneously but independently. The results are subsequently combined to create the final alignment. This approach allows DRAGMAP to handle more complex genomes, especially those with repetitive regions or large structural variations: repetitive regions can be difficult to align as they can produce multiple possible alignments in different regions of the genome. DRAGMAP also uses a more rigorous statistical approach than BWA-MEM which generally produces more accurate alignments in such difficult regions.

Intelliseq’s workflows use the BWA-MEM as the default tool for alignment. However, if you prefer to align your sample sequence using DRAGMAP, use the “Advanced” options when setting up the analysis. 

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[1] Heng Li and Richard Durbin (2009) “Fast and accurate short read alignment with Burrows–Wheeler transform” 





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