Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment.

Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA-mem parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA-aln is still the gold-standard for ancient DNA read alignment .