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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: scaffolding reads with practical algorithms.
Scarpa citations
(7)Approaches for in silico finishing of microbial genome sequences
[…] 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 […]
Genome of ‘Ca. Desulfovibrio trichonymphae', an H2 oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut
[…] 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 […]
Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
[…] 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 […]
Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi automated bioinformatics methods
[…] 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 […]
Exact approaches for scaffolding
[…] 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 […]
Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans
[…] 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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