Skip to main content

Table 2 Overview of aligner characteristics based on results from our experiments. Boldfaced values indicate the most desirable result across the different metrics. Brief comments on the characteristics of the aligners are included

From: Strobealign: flexible seed size enables ultra-fast and accurate read alignment

Category

Tool

%-correct\(\uparrow\)

%-aligned\(\uparrow\)

Speed\(\uparrow\)

Mem\(\downarrow\)

Comment on overall results

Traditional

BWA-MEM

High

High

Low

Low

Works well in all benchmarked scenarios. High accuracy, but slow

Bowtie2

High

Medium

Low

Low

Works well in most benchmarked scenarios but is slow. Skips to align many reads for high diversity datasets

Recent

Strobealign

High

High

High

High

A very fast aligner with high accuracy. Peak performance for 150–500nt reads. Not recommended for 50–75nt reads

BWA-MEM2

High

High

Low to medium

High

Identical output to BWA-MEM at 1.2–2x speedup for paired-end alignment (our experiments), but very high memory usage

minimap2

Medium

Medium

Medium

Medium

Relatively high accuracy on human genome, but not on repetitive genomes (rye and maize). Lower accuracy and slower than strobealign on most datasets but uses less memory

SNAP v2.0

Medium

Low

Medium to high

High

Good accuracy and speed for low diversity datasets. Poor accuracy, speed, and percent aligned reads for high diversity and on the biological datasets

Accel-Align

Low

Medium

High

High

A very fast aligner but with lowest accuracy overall out of the benchmarked aligners