5. Conclusion
In this study, we found that BWA mem with the parameter –k=19
and –r=2.5 is comparable to the BWA aln with MS parameters (18)
when considering the recovery of ancient DNA, but has a significantly
shorter running time than that of BWA aln with MS parameters. For
the recovery of endogenous DNA from the ancient sequencing data with
homologous contaminations, we recommend screening of reads with the
parameter –DeamNum=1, –DetectRange=15 and –DoubleOrSingle=or, which
will allow removal of more than 99% of homologous DNA contaminations
from the raw contaminated sequencing data. Overall, these
recommendations for ancient DNA mapping and separation of endogenous DNA
will benefit ancient DNA studies, especially for samples preserved under
poor conditions.
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