A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping

• The high levels of degradation characteristic of ancient DNA molecules severely hinder the recovery of endogenous DNA fragments and the discovery of genetic variation, limiting downstream population analyses. Optimization of read mapping strategies for ancient DNA is therefore essential to maximize the information we are able to recover from archaeological specimens. In this paper we assess Burrows-Wheeler Aligner (BWA) effectiveness for mapping of ancient DNA sequence data, comparing different sets of parameters and their effect on the number of endogenous sequences mapped and variants called. We also consider different filtering options for SNP calling, which include minimum values for depth of coverage and base quality in addition to mapping quality. Considering our results, as well as those of previous studies, we conclude that BWA-MEM is a good alternative to the current standard BWA-backtrack strategy for ancient DNA studies, especially when the computational resources are limited and time is a constraint. 

Subject headings

NATURVETENSKAP  -- Biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

HUMANIORA  -- Historia och arkeologi (hsv//swe)

HUMANITIES  -- History and Archaeology (hsv//eng)

Keyword

Alignment

Ancient DNA

BWA-aln

BWA-MEM

Variant calling

Publication and Content Type

ref (subject category)

kap (subject category)