Skip to main content
SpringerLink
Log in

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

  • Conference paper
  • First Online:
Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021) (PACBB 2021)

Part of the book series: Lecture Notes in Networks and Systems ((LNNS,volume 325))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Except for multiple threading (5), which was equally used in the four mapping procedures.

References

  1. Higuchi, R., Bowman, B., Freiberger, M., et al.: DNA sequences from the quagga, an extinct member of the horse family. Nature 312, 282–284 (1984). https://doi.org/10.1038/312282a0

    Article  Google Scholar 

  2. Mitchell, K.J., Rawlence, N.J.: Examining natural history through the lens of palaeogenomics. Trends Ecol. Evol. 36, 258–267 (2021). https://doi.org/10.1016/j.tree.2020.10.005

    Article  Google Scholar 

  3. Prüfer, K., Stenzel, U., Hofreiter, M., et al.: Computational challenges in the analysis of ancient DNA. Genome Biol. 11, R47 (2010). https://doi.org/10.1186/gb-2010-11-5-r47

    Article  Google Scholar 

  4. Günther, T., Nettelblad, C.: The presence and impact of reference bias on population genomic studies of prehistoric human populations. PLOS Genet. 15, e1008302 (2019). https://doi.org/10.1371/journal.pgen.1008302

    Article  Google Scholar 

  5. Gopalakrishnan, S., Samaniego Castruita, J.A., Sinding, M.-H.S., et al.: The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genom. 18, 495 (2017). https://doi.org/10.1186/s12864-017-3883-3

  6. Schubert, M., Ginolhac, A., Lindgreen, S., et al.: Improving ancient DNA read mapping against modern reference genomes. BMC Genom. 13, 178 (2012). https://doi.org/10.1186/1471-2164-13-178

    Article  Google Scholar 

  7. Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler trans-form. Bioinform. Oxf. Engl. 25, 1754–1760 (2009). https://doi.org/10.1093/bioinformatics/btp324

    Article  Google Scholar 

  8. Xu, W., Lin, Y., Zhao, K., et al.: An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data. Ecol. Evol. 11, 390–401 (2020). https://doi.org/10.1002/ece3.7056

    Article  Google Scholar 

  9. Li, H.: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (2013). http://arxiv.org/abs/1303.3997

  10. Poullet, M., Orlando, L.: Assessing DNA sequence alignment methods for characterizing ancient genomes and methylomes. Front. Ecol. Evol. 8 (2020). https://doi.org/10.3389/fevo.2020.00105

  11. Langmead, B., Salzberg, S.L.: Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923

    Article  Google Scholar 

  12. NovoAlign | Novocraft. http://www.novocraft.com/products/novoalign/. Accessed 13 Apr 2021

  13. Oliva, A., Tobler, R., Cooper, A., et al.: Systematic benchmark of ancient DNA read mapping. Brief Bioinform. (2021). https://doi.org/10.1093/bib/bbab076

    Article  Google Scholar 

  14. Davis, S.J.M., Svensson, E.M., Albarella, U., et al.: Molecular and osteometric sexing of cattle metacarpals: a case study from 15th century AD Beja, Portugal. J. Archaeol. Sci. 39, 1445–1454 (2012). https://doi.org/10.1016/j.jas.2011.12.003

    Article  Google Scholar 

  15. Rodríguez-Varela, R., Günther, T., Krzewińska, M., et al.: Genomic analyses of pre-European conquest human remains from the Canary Islands reveal close affinity to modern North Africans. Curr Biol 27, 3396-3402.e5 (2017). https://doi.org/10.1016/j.cub.2017.09.059

    Article  Google Scholar 

  16. Yang, D.Y., Eng, B., Waye, J.S., et al.: Improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539–543 (1998). https://doi.org/10.1002/(SICI)1096-8644(199804)105:4%3c539::AID-AJPA10%3e3.0.CO;2-1

    Article  Google Scholar 

  17. Dabney, J., Knapp, M., Glocke, I., et al.: Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 110, 15758–15763 (2013). https://doi.org/10.1073/pnas.1314445110

    Article  Google Scholar 

  18. Meyer, M., Kircher, M.: Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5 (2010). https://doi.org/10.1101/pdb.prot5448

  19. Günther, T., Valdiosera, C., Malmström, H., et al.: Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proc. Natl. Acad. Sci. U. S. A. 112, 11917–11922 (2015). https://doi.org/10.1073/pnas.1509851112

    Article  Google Scholar 

  20. Jónsson, H., Ginolhac, A., Schubert, M., et al.: mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013). https://doi.org/10.1093/bioinformatics/btt193

    Article  Google Scholar 

  21. Martin, M.: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011). https://doi.org/10.14806/ej.17.1.200

  22. Magoč, T., Salzberg, S.L.: FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011). https://doi.org/10.1093/bioinformatics/btr507

    Article  Google Scholar 

  23. bwa man page - General Commands | ManKier. https://www.mankier.com/1/bwa. Accessed 14 Apr 2021

  24. Li, H., Handsaker, B., Wysoker, A., et al.: The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). https://doi.org/10.1093/bioinformatics/btp352

    Article  Google Scholar 

  25. McKenna, A., Hanna, M., Banks, E., et al.: The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010). https://doi.org/10.1101/gr.107524.110

    Article  Google Scholar 

  26. Jun, G., Wing, M.K., Abecasis, G.R., Kang, H.M.: An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data. Genome Res. gr.176552.114 (2015). https://doi.org/10.1101/gr.176552.114

  27. Danecek, P., Bonfield, J.K., Liddle, J., et al.: Twelve years of SAMtools and BCFtools. GigaScience 10 (2021). https://doi.org/10.1093/gigascience/giab008

  28. McLaren, W., Gil, L., Hunt, S.E., et al.: The ensemble variant effect predictor. Genome Biol. 17, 122 (2016). https://doi.org/10.1186/s13059-016-0974-4

    Article  Google Scholar 

  29. Paten, B., Novak, A.M., Eizenga, J.M., Garrison, E.: Genome graphs and the evolution of genome inference. Genome Res. 27, 665–676 (2017). https://doi.org/10.1101/gr.214155.116

    Article  Google Scholar 

  30. Martiniano, R., Garrison, E., Jones, E.R., et al.: Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph. bioRxiv 782755 (2020). https://doi.org/10.1101/782755

Download references

Acknowledgments

We thank Ana Arruda, Catarina Viegas, Andrea Martins, Cleia Detry and Simon J.M. Davis for providing access to well-documented cattle specimens for ancient DNA analysis. This work received funding from: the project PORBIOTA- Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER); Fundação Nacional para a Ciência e a Tecnologia (FCT), Portugal, contract grant 2020.02754.CEECIND (C.G.), Norma Transitória contract grant DL 57/2016/CP1440/CT0029 (A.E.P.) and the ARCHAIC Project grant PTDC/CVTLIV/2827/2014 co-funded by COMPETE 2020 POCI-01-0145-FEDER-016647 and LISBOA-01-0145-FEDER-016647 (C.G.). This work was also supported by National Funds through FCT/MCTES under the UIDB/50027/2020 funding.

Author information

Authors and Affiliations

  1. Faculdade de Ciências, Universidade do Porto, Porto, Portugal

    Cindy Sarmento

  2. CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal

    Sílvia Guimarães, Ana Elisabete Pires, Catarina Ginja & Nuno A. Fonseca

  3. Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey

    Gülşah Merve Kılınç

  4. Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden

    Anders Götherström

Authors
  1. Cindy Sarmento
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sílvia Guimarães
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gülşah Merve Kılınç
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Anders Götherström
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ana Elisabete Pires
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Catarina Ginja
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nuno A. Fonseca
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Cindy Sarmento .

Editor information

Editors and Affiliations

  1. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  2. Superior de Ingeniería Informática, Universidade de Vigo, Escuela, Ourense, Spain

    Florentino Fdez-Riverola

  3. Department of Genetics and Genomics, United Arab Emirates University, Abu Dhabi, United Arab Emirates

    Mohd Saberi Mohamad

  4. BISITE, Digital Innovation Hub, University of Salamanca, Salamanca, Salamanca, Spain

    Roberto Casado-Vara

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Sarmento, C. et al. (2022). A Study on Burrows-Wheeler Aligner’s Performance Optimization for Ancient DNA Mapping. In: Rocha, M., Fdez-Riverola, F., Mohamad, M.S., Casado-Vara, R. (eds) Practical Applications of Computational Biology & Bioinformatics, 15th International Conference (PACBB 2021). PACBB 2021. Lecture Notes in Networks and Systems, vol 325. Springer, Cham. https://doi.org/10.1007/978-3-030-86258-9_11

Download citation

Publish with us

Policies and ethics

Search

Navigation