scaffold_builder protocols

scaffold_builder specifications

Information


Unique identifier OMICS_00046
Name scaffold_builder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Robert Edwards <>

Information


Unique identifier OMICS_00046
Name scaffold_builder
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Robert Edwards <>

Publication for scaffold_builder

scaffold_builder IN pipelines

 (2)
2017
PMCID: 5640839
PMID: 28814514
DOI: 10.1128/JVI.01058-17

[…] kit v2; 500 cycles). read pairs were quality checked and joined using fastqjoin software (69). de novo assembly was done using a5 assembler pipeline (70) under the default parameters, and the scaffold_builder tool (71) was used for scaffolding the contigs. the assembled genome was compared with that of the asfv parental virulent ba71 strain (genbank accession number kp055815.1) (46) using […]

2016
PMCID: 5062080
PMID: 27734962
DOI: 10.1038/srep35076

[…] 238 scaffolds had only 1 genetic marker mapped causing an undeterminable orientation., to improve the tt8 assembly, we originally used a published reference-guided scaffolding program, called scaffold_builder20, but we found that our non-chromosome leftover scaffolds and pe reads would map to repeat regions of the genome instead of making extensions, scaffolds, or filling gaps. instead, […]

scaffold_builder institution(s)
Computational Science Research Center, San Diego State University, San Diego, CA, USA

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