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IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data

Authors Enno Adler , Stefan Böttcher, Rita Hartel, Cederic Alexander Steininger

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  • Information systems → Data compression
Keywords
  • burrows-wheeler transform
  • self-indexes
  • external-memory

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Abstract

The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the BWT in terms of time and memory usage is key to these applications. We present a novel external-memory algorithm called Improved-Bucket Burrows-Wheeler transform (IBB) for constructing the BWT of DNA datasets with highly diverse sequence lengths. IBB uses a right-aligned approach to efficiently handle sequences of varying lengths, a tree-based data structure to manage relative insert positions and ranks, and fine buckets to reduce the necessary amount of input and output to external memory. Our experiments demonstrate that IBB is 10% to 40% faster than the best existing state-of-the-art BWT construction algorithms on most datasets while maintaining competitive memory consumption.

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Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger. IBB: Fast Burrows-Wheeler Transform Construction for Length-Diverse DNA Data. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/LIPIcs.SEA.2025.2

Author Details

Enno Adler
  • Paderborn University, Germany
Stefan Böttcher
  • Paderborn University, Germany
Rita Hartel
  • Paderborn University, Germany
Cederic Alexander Steininger
  • Paderborn University, Germany

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References

  1. Enno Adler, Stefan Böttcher, Rita Hartel, and Cederic Alexander Steininger. IBB. Software, (visited on 2025-06-30). URL: https://github.com/adlerenno/ibb
    Software Heritage Logo archived version
    full metadata available at: https://doi.org/10.4230/artifacts.23784
  2. Enno Adler, Stefan Böttcher, and Rita Hartel. String Partition for Building Long BWTs, 2024. URL: https://arxiv.org/abs/2406.10610.
  3. Markus J. Bauer, Anthony J. Cox, and Giovanna Rosone. Lightweight algorithms for constructing and inverting the BWT of string collections. Theor. Comput. Sci., 483:134-148, 2013. URL: https://doi.org/10.1016/J.TCS.2012.02.002.
  4. Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, and Taher Mun. Prefix-free parsing for building big BWTs. Algorithms Mol. Biol., 14(1):13:1-13:15, 2019. URL: https://doi.org/10.1186/S13015-019-0148-5.
  5. Michael Burrows and David Wheeler. A block-sorting lossless data compression algorithm. In Digital SRC Research Report. Citeseer, 1994. Google Scholar
  6. Jasbir Dhaliwal, Simon J. Puglisi, and Andrew Turpin. Trends in Suffix Sorting: A Survey of Low Memory Algorithms. In Thirty-Fifth Australasian Computer Science Conference, ACSC 2012, Melbourne, Australia, January 2012, pages 91-98, 2012. URL: http://crpit.scem.westernsydney.edu.au/abstracts/CRPITV122Dhaliwal.html.
  7. Diego Díaz-Domínguez and Gonzalo Navarro. Efficient construction of the BWT for repetitive text using string compression. Inf. Comput., 294:105088, 2023. URL: https://doi.org/10.1016/J.IC.2023.105088.
  8. Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications. Algorithms Mol. Biol., 14(1):6:1-6:15, 2019. URL: https://doi.org/10.1186/S13015-019-0140-0.
  9. Paolo Ferragina, Travis Gagie, and Giovanni Manzini. Lightweight Data Indexing and Compression in External Memory. In LATIN 2010: Theoretical Informatics, 9th Latin American Symposium, Oaxaca, Mexico, April 19-23, 2010. Proceedings, pages 697-710, 2010. URL: https://doi.org/10.1007/978-3-642-12200-2_60.
  10. Paolo Ferragina and Giovanni Manzini. Indexing compressed text. J. ACM, 52(4):552-581, 2005. URL: https://doi.org/10.1145/1082036.1082039.
  11. Johannes Fischer and Florian Kurpicz. Dismantling DivSufSort. In Proceedings of the Prague Stringology Conference 2017, Prague, Czech Republic, August 28-30, 2017, pages 62-76, 2017. URL: http://www.stringology.org/event/2017/p07.html.
  12. Ben Langmead and Steven L Salzberg. Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4):357-359, 2012. Google Scholar
  13. Ben Langmead, Cole Trapnell, Mihai Pop, and Steven L Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology, 10:1-10, 2009. Google Scholar
  14. Heng Li. Fast construction of FM-index for long sequence reads. Bioinform., 30(22):3274-3275, 2014. URL: https://doi.org/10.1093/BIOINFORMATICS/BTU541.
  15. Heng Li and Richard Durbin. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinform., 26(5):589-595, 2010. URL: https://doi.org/10.1093/BIOINFORMATICS/BTP698.
  16. Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, and Jun Wang. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25(15):1966-1967, 2009. URL: https://doi.org/10.1093/BIOINFORMATICS/BTP336.
  17. Felipe A. Louza, Simon Gog, and Guilherme P. Telles. Induced Suffix Sorting for String Collections. In 2016 Data Compression Conference, DCC 2016, Snowbird, UT, USA, March 30 - April 1, 2016, pages 43-52, 2016. URL: https://doi.org/10.1109/DCC.2016.27.
  18. Felipe A. Louza, Guilherme P. Telles, Simon Gog, Nicola Prezza, and Giovanna Rosone. gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections. Algorithms Mol. Biol., 15(1):18, 2020. URL: https://doi.org/10.1186/S13015-020-00177-Y.
  19. Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, Sze-Hang Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, et al. MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). BMC bioinformatics, 16:1-8, 2015. Google Scholar
  20. Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, and Johannes Köster. Sustainable data analysis with snakemake [version 2; peer review: 2 approved]. F1000Research, 10(33), 2021. URL: https://doi.org/10.12688/f1000research.29032.2.
  21. Ge Nong, Sen Zhang, and Wai Hong Chan. Two Efficient Algorithms for Linear Time Suffix Array Construction. IEEE Trans. Computers, 60(10):1471-1484, 2011. URL: https://doi.org/10.1109/TC.2010.188.
  22. Marco Oliva, Travis Gagie, and Christina Boucher. Recursive Prefix-Free Parsing for Building Big BWTs. In Data Compression Conference, DCC 2023, Snowbird, UT, USA, March 21-24, 2023, pages 62-70, 2023. URL: https://doi.org/10.1109/DCC55655.2023.00014.
  23. Simon J. Puglisi, William F. Smyth, and Andrew Turpin. A taxonomy of suffix array construction algorithms. In Proceedings of the Prague Stringology Conference, Prague, Czech Republic, August 29-31, 2005, pages 1-30, 2005. URL: http://www.stringology.org/event/2005/p1.html.
  24. Jared T Simpson and Richard Durbin. Efficient de novo assembly of large genomes using compressed data structures. Genome research, 22(3):549-556, 2012. Google Scholar
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