Scarpa

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]