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Documents authored by Schmidt, Sebastian

Document
DOI: 10.4230/LIPIcs.WABI.2024.8
Applying the Safe-And-Complete Framework to Practical Genome Assembly

Authors: Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.
Cite as

Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8,
  author =	{Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.},
  title =	{{Applying the Safe-And-Complete Framework to Practical Genome Assembly}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{8:1--8:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.8},
  URN =		{urn:nbn:de:0030-drops-206520},
  doi =		{10.4230/LIPIcs.WABI.2024.8},
  annote =	{Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation}
}
Document
DOI: 10.4230/LIPIcs.STACS.2023.17
Cut Paths and Their Remainder Structure, with Applications

Authors: Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, and Elia C. Zirondelli

Published in: LIPIcs, Volume 254, 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023)

Abstract
In a strongly connected graph G = (V,E), a cut arc (also called strong bridge) is an arc e ∈ E whose removal makes the graph no longer strongly connected. Equivalently, there exist u,v ∈ V, such that all u-v walks contain e. Cut arcs are a fundamental graph-theoretic notion, with countless applications, especially in reachability problems. In this paper we initiate the study of cut paths, as a generalisation of cut arcs, which we naturally define as those paths P for which there exist u,v ∈ V, such that all u-v walks contain P as subwalk. We first prove various properties of cut paths and define their remainder structures, which we use to present a simple O(m)-time verification algorithm for a cut path (|V| = n, |E| = m). Secondly, we apply cut paths and their remainder structures to improve several reachability problems from bioinformatics, as follows. A walk is called safe if it is a subwalk of every node-covering closed walk of a strongly connected graph. Multi-safety is defined analogously, by considering node-covering sets of closed walks instead. We show that cut paths provide simple O(m)-time algorithms verifying if a walk is safe or multi-safe. For multi-safety, we present the first linear time algorithm, while for safety, we present a simple algorithm where the state-of-the-art employed complex data structures. Finally we show that the simultaneous computation of remainder structures of all subwalks of a cut path can be performed in linear time, since they are related in a structured way. These properties yield an O(mn)-time algorithm outputting all maximal multi-safe walks, improving over the state-of-the-art algorithm running in time O(m²+n³). The results of this paper only scratch the surface in the study of cut paths, and we believe a rich structure of a graph can be revealed, considering the perspective of a path, instead of just an arc.
Cite as

Massimo Cairo, Shahbaz Khan, Romeo Rizzi, Sebastian Schmidt, Alexandru I. Tomescu, and Elia C. Zirondelli. Cut Paths and Their Remainder Structure, with Applications. In 40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 254, pp. 17:1-17:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{cairo_et_al:LIPIcs.STACS.2023.17,
  author =	{Cairo, Massimo and Khan, Shahbaz and Rizzi, Romeo and Schmidt, Sebastian and Tomescu, Alexandru I. and Zirondelli, Elia C.},
  title =	{{Cut Paths and Their Remainder Structure, with Applications}},
  booktitle =	{40th International Symposium on Theoretical Aspects of Computer Science (STACS 2023)},
  pages =	{17:1--17:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-266-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{254},
  editor =	{Berenbrink, Petra and Bouyer, Patricia and Dawar, Anuj and Kant\'{e}, Mamadou Moustapha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2023.17},
  URN =		{urn:nbn:de:0030-drops-176690},
  doi =		{10.4230/LIPIcs.STACS.2023.17},
  annote =	{Keywords: reachability, cut arc, strong bridge, covering walk, safety, persistence, essentiality, genome assembly}
}
Document
DOI: 10.4230/LIPIcs.WABI.2022.2
Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time

Authors: Sebastian Schmidt and Jarno N. Alanko

Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)

Abstract
A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e. without k-mer repetitions and in plain text). Recently, heuristics were presented to compute a near-minimum such representation. We present an algorithm to compute a minimum representation in optimal (linear) time and use it to evaluate the existing heuristics. For that, we present a formalisation of arc-centric bidirected de Bruijn graphs and carefully prove that it accurately models the k-mer spectrum of the input. Our algorithm first constructs the de Bruijn graph in linear time in the length of the input strings (for a fixed-size alphabet). Then it uses a Eulerian-cycle-based algorithm to compute the minimum representation, in time linear in the size of the output.
Cite as

Sebastian Schmidt and Jarno N. Alanko. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2022.2,
  author =	{Schmidt, Sebastian and Alanko, Jarno N.},
  title =	{{Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{2:1--2:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-243-3},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.2},
  URN =		{urn:nbn:de:0030-drops-170361},
  doi =		{10.4230/LIPIcs.WABI.2022.2},
  annote =	{Keywords: Spectrum preserving string sets, Eulerian cycle, Suffix tree, Bidirected arc-centric de Bruijn graph, k-mer based methods}
}
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