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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


No version available

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 citations

 (13)
call_split

BA71ΔCD2: a New Recombinant Live Attenuated African Swine Fever Virus with Cross Protective Capabilities

2017
J Virol
PMCID: 5640839
PMID: 28814514
DOI: 10.1128/JVI.01058-17
call_split See protocol

[…] Seq reagent kit v2; 500 cycles). Read pairs were quality checked and joined using fastqjoin software (). De novo assembly was done using A5 assembler pipeline () under the default parameters, and the scaffold_builder tool () 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) () using Arte […]

library_books

Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus

2017
Genome Announc
PMCID: 5255918
PMID: 28104661
DOI: 10.1128/genomeA.01493-16

[…] genome 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 g […]

library_books

Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

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

[…] entation, 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, we b […]

library_books

Contig Layout Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

2016
PLoS One
PMCID: 4889084
PMID: 27248146
DOI: 10.1371/journal.pone.0155459

[…] s to directly ordering the contigs according to a chosen reference to build a chromosomal assembly with the help of tools such as ABACAS [], Ragout [], Mauve Contig Mover (MCM) [], CONTIGuator [] and Scaffold_builder [] etc. These reference based approaches are known to be very efficient in analyzing specific mutations/variations among highly similar organisms since the possibilities of finding no […]

call_split

HHV 8 unrelated primary effusion like lymphoma associated with clonal loss of inherited chromosomally integrated human herpesvirus 6A from the telomere of chromosome 19q

2016
Sci Rep
PMCID: 4779988
PMID: 26947392
DOI: 10.1038/srep22730
call_split See protocol

[…] mina) 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 Sang […]

call_split

Genome Sequences of Two Pseudorabies Virus Strains Isolated in Greece

2016
Genome Announc
PMCID: 4722279
PMID: 26798112
DOI: 10.1128/genomeA.01624-15
call_split See protocol

[…] 025.4) 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 gaps […]

Citations

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

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