Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes
Ilya Minkin,Ilya Minkin,Anand Patel,Anand Patel,Mikhail Kolmogorov,Mikhail Kolmogorov,Nikolay Vyahhi,Nikolay Vyahhi,Son Pham,Son Pham +9 more
- pp 215-229
TLDR
Sibelia is a tool for finding synteny blocks in multiple closely related microbial genomes using iterative de Bruijn graphs that can find synteny Blocks that are repeated within genomes as well as blocks shared by multiple genomes.Abstract:
Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we present Sibelia, a tool for finding synteny blocks in multiple closely related microbial genomes using iterative de Bruijn graphs. Unlike most other tools, Sibelia can find synteny blocks that are repeated within genomes as well as blocks shared by multiple genomes. It represents synteny blocks in a hierarchy structure with multiple layers, each of which representing a different granularity level. Sibelia has been designed to work efficiently with a large number of microbial genomes; it finds synteny blocks in 31 S. aureus genomes within 31 minutes and in 59 E.coli genomes within 107 minutes on a standard desktop. Sibelia software is distributed under the GNU GPL v2 license and is available at: https://github.com/bioinf/Sibelia. Sibelia’s web-server is available at: http://etool.me/software/sibelia.read more
Citations
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Journal ArticleDOI
Assembly of long error-prone reads using de Bruijn graphs.
TL;DR: An algorithmic approach for assembling long error-prone reads is proposed and the ABruijn assembler is described, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.
Journal ArticleDOI
Computational pan-genomics: status, promises and challenges.
Tobias Marschall,Manja Marz,Manja Marz,Thomas Abeel,Louis Dijkstra,Bas E. Dutilh,Ali Ghaffaari,Ali Ghaffaari,Paul Kersey,Wigard P. Kloosterman,Veli Mäkinen,Adam M. Novak,Benedict Paten,David Porubsky,Eric Rivals,Can Alkan,Jasmijn A. Baaijens,Paul I.W. de Bakker,Valentina Boeva,Raoul J. P. Bonnal,Francesca Chiaromonte,Rayan Chikhi,Francesca D. Ciccarelli,Robin Cijvat,Erwin Datema,Cornelia M. van Duijn,Evan E. Eichler,Evan E. Eichler,Corinna Ernst,Eleazar Eskin,Erik Garrison,Mohammed El-Kebir,Gunnar W. Klau,Jan O. Korbel,Eric-Wubbo Lameijer,Benjamin Langmead,Marcel Martin,Paul Medvedev,John C. Mu,Pieter B. Neerincx,Klaasjan G. Ouwens,Pierre Peterlongo,Nadia Pisanti,Sven Rahmann,Ben Raphael,Knut Reinert,Dick de Ridder,Jeroen de Ridder,Matthias Schlesner,Ole Schulz-Trieglaff,Ashley D. Sanders,Siavash Sheikhizadeh,Carl Shneider,Sandra Smit,Daniel Valenzuela,Jiayin Wang,Lodewyk F. A. Wessels,Y. Zhang,Victor Guryev,Fabio Vandin,Kai Ye,Alexander Schönhuth +61 more
TL;DR: Already available approaches to construct and use pan-genomes are examined, the potential benefits of future technologies and methodologies are discussed, and open challenges from the vantage point of the above-mentioned biological disciplines are reviewed.
Journal ArticleDOI
Ragout—a reference-assisted assembly tool for bacterial genomes
TL;DR: Ragout is presented, a genome rearrangement approach that believes that for common bacterial species, where many complete genome sequences from related strains have been available, the current high-throughput short-read sequencing paradigm is sufficient to obtain a single high-quality scaffold for each chromosome.
Journal ArticleDOI
SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
TL;DR: An algorithm is introduced that directly constructs the compressed de Bruijn graph in time and space linear to the total number of genomes for a given maximum genome size and is demonstrated by analyzing the nine-strain pan-genome of Bacillus anthracis and up to 62 strains of Escherichia coli.
Journal ArticleDOI
Chromosome assembly of large and complex genomes using multiple references.
Mikhail Kolmogorov,Joel Armstrong,Brian J. Raney,Ian Streeter,Matthew Dunn,Fengtang Yang,Duncan T. Odom,Duncan T. Odom,Paul Flicek,Paul Flicek,Thomas M. Keane,Thomas M. Keane,Thomas M. Keane,David Thybert,David Thybert,Benedict Paten,Son Pham +16 more
TL;DR: Ragout 2 transformed three sets of contigs into chromosome-scale assemblies with accuracy comparable to chromosome assemblies generated in the original study using BioNano maps, Hi-C, BAC clones, and FISH.
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