Protocols

Irys-scaffolding specifications

Information


Unique identifier OMICS_30105
Name Irys-scaffolding
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.1.0
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Susan J. Brown

Publication for Irys-scaffolding

Irys-scaffolding citations

 (2)
library_books

OMSim: a simulator for optical map data

2017
Bioinformatics
PMCID: 5860066
PMID: 28472230
DOI: 10.1093/bioinformatics/btx293

[…] consensus maps involves the alignment of the molecules such that the label positions match. The Irys Software System (http://bionanogenomics.com/wp-content/uploads/2015/01/datasheet-web.pdf) and the Irys-scaffolding scripts () can be used to automate this procedure.We developed OMSim to generate synthetic optical map data. This serves two purposes. First, OMSim can assist in the development and b […]

call_split

An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance

2017
Plant Biotechnol J
PMCID: 5506647
PMID: 28111887
DOI: 10.1111/pbi.12697
call_split See protocol

[…] The complete pipeline of the Stitch algorithm by Shelton et al. () (https://github.com/i5K-KINBRE-script-share/Irys-scaffolding/blob/master/KSU_bioinfo_lab/assemble_XeonPhi/assemble_XeonPhi_LAB.md) was run on the online cluster zythos provided by the Pawsey Supercomputing Center, Western Australia. The first d […]

Irys-scaffolding institution(s)
KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA; BioNano Genomics, San Diego, CA, USA
Irys-scaffolding funding source(s)
Supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20 GM103418.

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