Ragout protocols

Ragout computational protocol

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 pipelines

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

[…] sequences. selected v. fischeri gdna-spiked samples were subjected to de novo assembly with spades 3.9 (34). the resulting contigs were qualified with quast 4.3 (35) and further scaffolded with ragout 1.2 (36) 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 (37). […]

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

[…] the output maf files were filtered for 1:1 ortholog alignments using single_cov2 [88]. subsequently, we combined pairwise alignments into multiple alignments using the multiz tool [89]. we then used ragout [90] 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 […]

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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