In the preprint, I found information that panmap implements bwa-aln as the preferred algorithm for short ancient DNA reads. However, in the documentation, I found information that it uses bwa-mem.
Which algorithm is actually implemented?
Also, would it be possible to add an option to manually specify parameters for the aligner?
In the preprint, I found information that panmap implements bwa-aln as the preferred algorithm for short ancient DNA reads. However, in the documentation, I found information that it uses bwa-mem.
Which algorithm is actually implemented?
Also, would it be possible to add an option to manually specify parameters for the aligner?