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

Adrien Oliva; Raymond Tobler; Bastien Llamas; Yassine Souilmi

doi:10.1002/ece3.8297

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

Ecol Evol. 2021 Dec 17;11(24):18743-18748. doi: 10.1002/ece3.8297. eCollection 2021 Dec.

Authors

Adrien Oliva¹, Raymond Tobler^{1

2}, Bastien Llamas^{1

2

3}, Yassine Souilmi^{1

2

3}

Affiliations

¹ Australian Centre for Ancient DNA School of Biological Sciences Faculty of Sciences The University of Adelaide Adelaide South Australia Australia.
² The Environment Institute Faculty of Sciences The University of Adelaide Adelaide South Australia Australia.
³ National Centre for Indigenous Genomics Australian National University Canberra Australian Capital Territory Australia.

Abstract

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 .