Ragout statistics

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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


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  • person_outline Son Pham <>
  • person_outline David Thybert <>

Publications for Reference-Assisted Genome Ordering UTility

Ragout in pipeline

PMCID: 4833346
PMID: 27082250
DOI: 10.1371/journal.pgen.1005954

[…] []. the output maf files were filtered for 1:1 ortholog alignments using single_cov2 []. subsequently, we combined pairwise alignments into multiple alignments using the multiz tool []. we then used ragout [] to infer the order of asian sea bass contigs according to colinearity with g. aculeatus and d. labrax assuming a closer relationship of d. labrax and l. calcarifer. the ordered contigs […]

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Ragout in publications

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

[…] 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 […]

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

[…] 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 […]

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

[…] assemblers. the winning assembly computed by spades [] for both data sets, as well as the minia assemblies on both datasets, were subsequently used as input for two comparative scaffolding programs, ragout [] and medusa [], to obtain a scaffolding of the initial contigs considering the extant reference genomes in a phylogenetic context. for all scaffolds, we ran gap2seq [] to close the gaps. […]

PMCID: 4807235
PMID: 27013046
DOI: 10.1128/genomeA.00164-16

[…] were generated, resulting in 54-fold coverage, with average quality scores (phred) of 33.7. de novo assembly was performed using spades version 3.5.0 (). the resulting contigs were ordered with ragout version 0.2 () using actinoplanes sp. strain n902-109 (genbank accession no. prjna198760) as the reference genome. the assembly was improved by remapping reads using pilon version 1.12 (). […]

PMCID: 4270482
PMID: 25521852
DOI: 10.1371/journal.pgen.1004874

[…] remaps individual short reads to de novo assemblies in order to account for snp miscalling by assemblers, but that method also requires extensive manual curation. another recently described method, ragout , may be more suited for automated pipelines because it does not require manual intervention. however, we do not know of a direct demonstration that ragout can accurately handle […]

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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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