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AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors Adam Cicherski , Anna Lisiecka , Norbert Dojer

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Author Details

Adam Cicherski
  • Institute of Informatics, University of Warsaw, Poland
Anna Lisiecka
  • Institute of Informatics, University of Warsaw, Poland
Norbert Dojer
  • Institute of Informatics, University of Warsaw, Poland

Funding

This work was supported by the National Science Centre, Poland, under grant number 2022/47/B/ST6/03154.

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Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024) https://doi.org/10.4230/LIPIcs.WABI.2024.23

Abstract

The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections.
In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.

Subject Classification

ACM Subject Classification
  • Applied computing → Computational genomics
Keywords
  • pangenome
  • variation graph
  • genome alignment
  • population genomics

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References

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    Software Heritage Logo archived version
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