Safe and Complete Contig Assembly Via Omnitigs

@article{Tomescu2016SafeAC,
  title={Safe and Complete Contig Assembly Via Omnitigs},
  author={Alexandru I. Tomescu and Paul Medvedev},
  journal={ArXiv},
  year={2016},
  volume={abs/1601.02932}
}
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be… 
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12 Citations
Highly Influential Citations
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Background Citations
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Methods Citations
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Results Citations
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12 Citations

Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time

TLDR
A surprising $O(m)$-time algorithm to identify all maximal omnitigs of a graph with $n$ nodes and $m$ arcs, notwithstanding the existence of families of graphs with $\Theta(mn)$ total maximal Omnitig size.

A safe and complete algorithm for metagenomic assembly

TLDR
A safe and complete algorithm finding all safe walks of G, which constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.

Assembling Omnitigs using Hidden-Order de Bruijn Graphs

TLDR
A succinct representation of that array's Cartesian tree, which takes only 2 extra bits per edge and still lets us support interesting navigation operations efficiently and extract a set of safe strings more informative than the unitigs, while using a reasonable amount of memory.

Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful

TLDR
This paper is the first to theoretically predict the existence of these assembler artifacts and confirm and measure the extent of their occurrence in practice, and it is proved that, contrary to popular belief, unitigs are not always safe.

From omnitigs to macrotigs: a linear-time algorithm for safe walks - common to all closed arc-coverings of a directed graph

TLDR
An O(m)-time algorithm to identify all maximal omnitigs, thanks to the discovery of a family of walks (macrotigs) with the property that all the non-trivial omnitig are univocal extensions of subwalks of a macrotig.

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph

TLDR
New insights about the structure of omnitigs are proved and several open questions about them are solved to achieve an O(nm)-time algorithm for outputting all the maximal omnitig of a graph (with n nodes and m edges).

deGSM: memory scalable construction of large scale de Bruijn Graph

TLDR
The experimental results demonstrate that the proposed lightweight parallel de Bruijn graph construction approach, deGSM, is able to handle very large genome sequence(s), e.g., the contigs and scaffolds recorded in Gen-Bank database and Picea abies HTS dataset.

Safely Filling Gaps with Partial Solutions Common to All Solutions

TLDR
This work gives an efficient safe algorithm for reliable gap filling: filling gaps with those sub-paths common to all gap filling solutions, following the framework of (Tomescu and Medvedev, RECOMB 2016).

deBWT: parallel construction of Burrows–Wheeler Transform for large collection of genomes with de Bruijn-branch encoding

TLDR
The benchmarking suggests that, deBWT is efficient and scalable to construct BWT for large dataset by parallel computing, and well-suited to index many genomes, such as a collection of individual human genomes, with multiple-core servers or clusters.

Safety in s-t Paths, Trails and Walks

TLDR
It is proved that there exists a compact representation computable in linear time, that allows outputting all maximal safe walks in time linear in their length, and that the same complexity results hold for the analogous generalisations of s-tarticulation points (nodes appearing in all s-T paths).

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