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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