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PLEASE READ: SSPACE tracks in memory all contigs. That means that the memory usage will increase drastically with the size of your contig data set. In addition, during contig extension single reads are extracted and mapped to the contigs. Unmapped reads are stored in memory. Again, the more reads that can not map. 12 Dec We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime , multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows  Abstract - INTRODUCTION - METHODS - RESULTS. Bioinformatics. Feb 15;27(4) doi: /bioinformatics/btq Epub Dec Scaffolding pre-assembled contigs using SSPACE. Boetzer M(1), Henkel CV, Jansen HJ, Butler D, Pirovano W. Author information: (1) BaseClear B.V., Einsteinweg 5, CC Leiden, Leiden,The Netherlands. SUMMARY: De.

SSPACE, developed by BaseClear, is a stand-alone program for scaffolding pre- assembled contigs using NGS paired-read data. By using the distance information of paired-end data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. A stand-alone program for scaffolding pre-assembled contigs using NGS paired- read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and . 10 Dec during my Master thesis I developed a stand-alone scaffolding tool named SSPACE for scaffolding pre-assembled contigs using paired-read data. I developed this program since I couldn't find a program which was able to do this, except from Bambus. However, we had lots of issues on Bambus, including.

SSPACE library file is a simple text file with following information in space separated format. NameTag Aligner(bwa or bowtie) Fastq1 Fastq2 AverageInserSize Error OrientationIndication. A sample command would look like this. Lib1 bwa FR. You can use SPAdes. 25 Oct Sspace Data Members. Scalar Values. @coefcov(i,j) covariance of coefficients i and j. @coefs(i) coefficient i. @eqregobs(k) number of observations in signal equation k. @linecount scalar containing the number of lines in the Sspace object. @sddep(k) standard deviation of the signal variable in equation k. 7 Feb Description. "SSPACE is a stand-alone program for scaffolding pre-assembled contigs using paired-read data. It is unique in offering the possibility to manually control the scaffolding process." more at SSPACE.

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