Ragout pipeline

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
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.1
Stability Stable
Requirements NetworkX Python, Newick Python parser, Sibelia
Maintained Yes


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  • person_outline Son Pham <>

Publication for Reference-Assisted Genome Ordering UTility

Ragout citation

PMCID: 4833346

[…] 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, UCSD, La Jolla, CA, USA

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