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Ragout specifications


Unique identifier OMICS_07883
Name Ragout
Alternative name Reference-Assisted Genome Ordering UTility
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
License BSD 2-clause “Simplified” License, GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.1
Stability Stable
NetworkX Python, Newick Python parser, Sibelia
Maintained Yes


No version available



  • person_outline Son Pham
  • person_outline David Thybert

Publications for Reference-Assisted Genome Ordering UTility

Ragout citations


Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe

Front Microbiol
PMCID: 5895724
PMID: 29675009
DOI: 10.3389/fmicb.2018.00656

[…] y, the Illumina reads of the 12 European strains were processed with Edena (Hernandez et al., ). From the same datasets, full genomes were drafted with SPAdes (Bankevich et al., ) and scaffolded with Ragout (Kolmogorov et al., ) having the complete genome of CRAFRU 14.08 as a reference. Using Mauve and MUMmer the drafts were aligned to complete genomes, visualized and the polymorphic regions expor […]


KatharoSeq Enables High Throughput Microbiome Analysis from Low Biomass Samples

PMCID: 5864415
PMID: 29577086
DOI: 10.1128/mSystems.00218-17

[…] processed sequences. Selected V. fischeri gDNA-spiked samples were subjected to de novo assembly with SPAdes 3.9 (). The resulting contigs were qualified with QUAST 4.3 () and further scaffolded with Ragout 1.2 () against the V. fischeri ES114 reference genome (RefSeq accession no. GCF_000011805.1). The resulting draft genomes were aligned with the reference genome by using Brig 0.95 (). Default p […]


Draft Genome Sequences of Escherichia coli Isolates from India

Genome Announc
PMCID: 5814501
PMID: 29449387
DOI: 10.1128/genomeA.00047-18

[…] rated using the Contig Integrator for Sequence Assembly (CISA). This yielded 136 and 179 contigs for Escherichia coli strains 360/16 and 646, respectively. These contigs were finally rearranged using Reference-Assisted Genome Ordering Utility (Ragout) version 2.0 to obtain the draft genomes of 4,748,376 bp and 5,320,632 bp for Escherichia coli strains 360/16 and 646, respectively. Annotation of th […]


Draft Genome Sequence of the Mucoid Pseudomonas aeruginosa Clinical Isolate PA34

Genome Announc
PMCID: 5690347
PMID: 29146840
DOI: 10.1128/genomeA.01307-17

[…] GenBank accession no. CP007224, AP014839, CP012066, CP002496, CP007147, NC_011770, CP014948, and CP007399). Specifically, an initial de novo assembly was generated using SPAdes 3.10 and improved with RAGOUT to inform contig order and AlignGraph to close the gaps between scaffolds (). The assembly was improved through iterative remapping of the reads to the assembly using iCORN2 to correct amplific […]


Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

Microb Genom
PMCID: 5643016
PMID: 29114402
DOI: 10.1099/mgen.0.000123

[…] mbly likelihood according to both the lap [] and cgal [] score. The MeDuSa scaffolder was not able to estimate the gap sizes needed as input for Gap2Seq. Hence, the better likelihood in comparison to Ragout can be accounted to the missing gaps characterized by Ns in the Ragout assembly. Also worth noting with the Marseille strain, MeDuSa was not able to correct a larger than expected contig assemb […]


A comparative evaluation of genome assembly reconciliation tools

Genome Biol
PMCID: 5436433
PMID: 28521789
DOI: 10.1186/s13059-017-1213-3

[…] erature that are no longer maintained and/or have no documentation were excluded from our evaluation. We also excluded GAM, because it was superseded by GAM_NGS. Other tools such as eRGA [], MAIA [], RAGOUT [], and Minimus2 [] were also not included in our comparative evaluation because these tools address different problems. Reference-guided assembly (eRGA, RAGOUT, and MAIA) and hybrid assembly ( […]


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Ragout institution(s)
Department of Computer Science and Engineering, University of California, San Diego, CA, USA; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; School of Life Sciences, University of Nottingham, Nottingham, United Kingdom; Earlham Institute, Norwich Research Park, Norwich, UK; BioTuring Incorporated, San Diego, CA, USA
Ragout funding source(s)
Supported by the Wellcome Trust (WT108749/Z/15/ Z, WT098051, WT202878/B/16/Z), the National Human Genome Research Institute (U41HG007234), and the European Molecular Biology Laboratory, the European Community’s Seventh Framework Programme (FP7/2010-2014) under grant agreement 244356 (NextGen) and from the European Union’s Seventh Framework Programme (FP7/2007–2013) under grant agreement HEALTH-F4-2010-241504 (EURATRANS), and the National Institutes of Health (3U54HG007990, 1U01HL137183, and 5U41HG007234) and the W.M. Keck Foundation (DT06172015).

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