Why is bwa-aln used for ancient DNA reads?

BWA implements three algorithms: bwa-aln , bwa-sw and bwa-mem . Although bwa-aln is the oldest, it remains a popular choice for ancient DNA (aDNA) data. Is it because researchers working on aDNA are too lazy to change? Not quite. The following plot from Dolenz et al (2024) shows the mismatch rate as a function of read length for reads mapped with mapping quality (mapQ) 25 or higher. This plot…