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DOI: 10.4230/LIPIcs.WABI.2022.19

Pangenomic Genotyping with the Marker Array

Authors: Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead

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

Abstract

We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while avoiding the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods.

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Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead. Pangenomic Genotyping with the Marker Array. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{mun_et_al:LIPIcs.WABI.2022.19,
  author =	{Mun, Taher and Vaddadi, Naga Sai Kavya and Langmead, Ben},
  title =	{{Pangenomic Genotyping with the Marker Array}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{19:1--19:17},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.19},
  URN =		{urn:nbn:de:0030-drops-170530},
  doi =		{10.4230/LIPIcs.WABI.2022.19},
  annote =	{Keywords: Sequence alignment indexing genotyping}
}

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DOI: 10.4230/LIPIcs.ESA.2021.56

Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing

Authors: Dominik Kempa and Ben Langmead

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)

Abstract

Grammar compression is, next to Lempel-Ziv (LZ77) and run-length Burrows-Wheeler transform (RLBWT), one of the most flexible approaches to representing and processing highly compressible strings. The main idea is to represent a text as a context-free grammar whose language is precisely the input string. This is called a straight-line grammar (SLG). An AVL grammar, proposed by Rytter [Theor. Comput. Sci., 2003] is a type of SLG that additionally satisfies the AVL property: the heights of parse trees for children of every nonterminal differ by at most one. In contrast to other SLG constructions, AVL grammars can be constructed from the LZ77 parsing in compressed time: 𝒪(z log n) where z is the size of the LZ77 parsing and n is the length of the input text. Despite these advantages, AVL grammars are thought to be too large to be practical. We present a new technique for rapidly constructing a small AVL grammar from an LZ77 or LZ77-like parse. Our algorithm produces grammars that are always at least five times smaller than those produced by the original algorithm, and usually not more than double the size of grammars produced by the practical Re-Pair compressor [Larsson and Moffat, Proc. IEEE, 2000]. Our algorithm also achieves low peak RAM usage. By combining this algorithm with recent advances in approximating the LZ77 parsing, we show that our method has the potential to construct a run-length BWT in about one third of the time and peak RAM required by other approaches. Overall, we show that AVL grammars are surprisingly practical, opening the door to much faster construction of key compressed data structures.

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Dominik Kempa and Ben Langmead. Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 56:1-56:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{kempa_et_al:LIPIcs.ESA.2021.56,
  author =	{Kempa, Dominik and Langmead, Ben},
  title =	{{Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{56:1--56:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2021.56},
  URN =		{urn:nbn:de:0030-drops-146373},
  doi =		{10.4230/LIPIcs.ESA.2021.56},
  annote =	{Keywords: grammar compression, straight-line program, SLP, AVL grammar, Lempel-Ziv compression, LZ77, dictionary compression}
}

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Documents authored by Langmead, Ben

Pangenomic Genotyping with the Marker Array

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Fast and Space-Efficient Construction of AVL Grammars from the LZ77 Parsing

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