Scaffolder specifications


Unique identifier OMICS_25071
Name Scaffolder
Software type Application/Script
Interface Application programming interface
Restrictions to use None
Input data A set of nucleotide sequences.
Output format YAML
Operating system Unix/Linux, Mac OS
Programming languages Ruby
License MIT License
Computer skills Advanced
Stability Stable
RubyGems, BioRuby, confligliere, ronn
Maintained Yes




No version available



  • person_outline Scaffolder Team

Publication for Scaffolder

Scaffolder citations


Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray Finned Fishes

Genome Biol Evol
PMCID: 4684697
PMID: 26446539
DOI: 10.1093/gbe/evv186

[…] 30 bp were assembled and scaffolded using the MSR-CA genome assembler (now renamed MaSuRCA, with default settings) (). Further scaffolding was carried out with reads from the mate-pair library using Scaffolder (). The final draft assembly consists of scaffolds longer than 200 bp. Finally, the CEGMA program () was used to assess the completeness of the assembly by detecting the presence of 248 hig […]


Genomer — A Swiss Army Knife for Genome Scaffolding

PLoS One
PMCID: 3691230
PMID: 23826173
DOI: 10.1371/journal.pone.0066922

[…] Mac OS X and Linux systems. The latest version of Genomer can installed from the Rubygems package management system with the command gem install genomer. Genomer is based on our previously described “Scaffolder” software and is invoked on the command line with the command genomer. Genomer provides extensive documentation via UNIX manual pages and on the Genomer website at […]

Scaffolder institution(s)
Biology Department, The University of Akron, Akron, OH, USA
Scaffolder funding source(s)
Supported by the National Institute for Health: IDeA Network of Biomedical Research Excellence (KY-INBRE) grant (NIH 2P20 RR016481-09) and the NIH R15 AREA Program grant (R15GM079775).

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