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Scarpa specifications

Information


Unique identifier OMICS_00047
Name Scarpa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Scarpa

Scarpa citations

 (7)
library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] tions between different contigs using the relative-orientation information and the estimated insert-size. ABySS (), SOPRA (), SOAPdenovo (), Bambus 2 (), MIP (), Opera (), SSPACE (), SLIQ (), SGA (), SCARPA (), WiseScaffolder () and ScaffoldScaffolder () are examples of scaffolding tools based on paired-end information. More recently, the use of long-reads was also incorporated into scaffolding to […]

library_books

Genome of ‘Ca. Desulfovibrio trichonymphae', an H2 oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut

2016
PMCID: 5322295
PMID: 27801909
DOI: 10.1038/ismej.2016.143

[…] imming using programs cutadapt and prinseq, respectively (; ). The reads were assembled into contigs, using SPAdes 3.0 (), and the contigs and the mate-pair reads were used to generate scaffolds with SCARPA 0.241 (). Finding and functional annotation of genes were performed using MiGAP (http://www.migap.org), and the result was curated manually. Pseudogenes were manually identified as described pr […]

library_books

Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA

2016
Genome Biol Evol
PMCID: 5174739
PMID: 27635050
DOI: 10.1093/gbe/evw227

[…] a MiSeq platform using the MiSeq Reagent Kit v3 (600 cycles). The generated reads were quality-filtered and assembled into contigs using SPAdes 3.1 (), which were further assembled to scaffolds using SCARPA 0.241 (). Gaps in scaffolds were closed by PCR amplification and Sanger sequencing on ABI3730 Genetic Analyzers. Detailed procedures are described in the supplementary methods (Supplementary Ma […]

library_books

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi automated bioinformatics methods

2016
BMC Genomics
PMCID: 4793746
PMID: 26984673
DOI: 10.1186/s12864-016-2579-4

[…] ences remains a substantial endeavor []. Several automated programs have been developed to improve draft genome sequence assemblies such as Bambus [], SOPRA [], MIP [], SSPACE [], Opera [], GRASS [], SCARPA [], SSPACE-LongRead [], SOAP-de-novo2 [], GapFiller [] and PAGIT []. However, these programs were designed for assembling contigs into scaffolds and/or filling unknown regions, and are running […]

library_books

Exact approaches for scaffolding

2015
BMC Bioinformatics
PMCID: 4603742
PMID: 26451725
DOI: 10.1186/1471-2105-16-S14-S2

[…] r programming (MIP) as in [] and an expectation-maximization process to counter the intractability of the MIP model. They obtain results which are intermediary in quality between SSPACE and Opera. In SCARPA [], the two problems of orienting and ordering the contigs are separated, as in SOPRA. Transforming the graph such that the contig orientation problem has a feasible solution is a fixed-paramet […]

library_books

Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans

2014
PLoS Negl Trop Dis
PMCID: 3998919
PMID: 24763283
DOI: 10.1371/journal.pntd.0002728

[…] number of rearrangements to exist between the wMel and wGmm genomes. Breaking the scaffold makes allowance for these gaps. Finally, scaffolding was then performed on this reduced set of contigs using SCARPA with the Hi-Seq mate-pair libraries. The statistics for the assembly at each stage of the process are given in .The genome was annotated with XBASE and RAST , , followed by manual curation. Pu […]

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Scarpa institution(s)
Department of Computer Science, University of Toronto, Toronto, ON, Canada

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