scaffold_builder protocols

View scaffold_builder computational protocol

scaffold_builder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Assembly scaffolding chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

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)
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_builder, 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, […]

2015
PMCID: 4513153
PMID: 26205859
DOI: 10.1128/genomeA.00799-15

[…] were available, it was decided to produce zgt-1 scaffolds based on the genome sequence of geobacillus kaustophilus hta426 (genbank accession number nc_006510.1). this was conducted online with the scaffold_builder tool () using default settings. this resulted in a new assembly with 241 scaffolds and a total length 3,483,107 bp. on this final assembly, gene prediction was carried […]


To access a full list of citations, you will need to upgrade to our premium service.

scaffold_builder in publications

 (8)
PMCID: 5255918
PMID: 28104661
DOI: 10.1128/genomeA.01493-16

[…] using cisa (contigs less than 1 kb were removed) (), and this was later aligned to the previously published a. macyae dsm 16346 genome (genbank accession no. lelk01000000) and scaffolded using scaffold_builder version 2.2 (). annotation of the genomes was performed using the ncbi prokaryotic genome annotation pipeline after sequence submission to genbank. although the g+c mol% of the four […]

PMCID: 4779988
PMID: 26947392
DOI: 10.1038/srep22730

[…] or an iontorrent personal genome sequencer (life technologies). the miseq read data for 1501-bl were assembled de novo into contigs by using abyss v. 1.5.2. a draft sequence was generated using scaffold builder to order the contigs against the reference hhv-6a strain u1102 sequence (nc_001664). gaps were closed by using megamerger, gapfiller v. 1–11 and custom perl scripts, or by manual […]

PMCID: 4722279
PMID: 26798112
DOI: 10.1128/genomeA.01624-15

[…] were removed by using bwa version 0.6.2-r126 (). the remaining reads (3,842,770 reads for strain kolchis, and 2,031,656 reads for strain hercules) were assembled de novo using spades 3.5.0 (). scaffold_builder () was used to produce a draft genome sequence by scaffolding the resulting contigs against the sequence of strain kaplan (genbank accession no. jq809328.1 []), and the remaining […]

PMCID: 4513153
PMID: 26205859
DOI: 10.1128/genomeA.00799-15

[…] were available, it was decided to produce zgt-1 scaffolds based on the genome sequence of geobacillus kaustophilus hta426 (genbank accession number nc_006510.1). this was conducted online with the scaffold_builder tool () using default settings. this resulted in a new assembly with 241 scaffolds and a total length 3,483,107 bp. on this final assembly, gene prediction was carried […]

PMCID: 4454671
PMID: 26039056
DOI: 10.1371/journal.pone.0126883

[…] enteritidis lk5 was scaffolded to the enteritidis p125109 sequence (accession no. am933172 []), and dublin sarb12 was scaffolded to the dublin ct02021853 sequence (accession no. cp001144 []) using scaffold_builder []. after the order of contigs around each chromosome was determined, draft genome sequences were assembled using a custom script with the gaps between contigs filled with n’s. draft […]


To access a full list of publications, you will need to upgrade to our premium service.

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

scaffold_builder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review scaffold_builder