Scaffolding pre-assembled contigs using SSPACE
De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Alt...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2011-02, Vol.27 (4), p.578-579 |
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| container_title | Bioinformatics (Oxford, England) |
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| creator | BOETZER, Marten HENKEL, Christiaan V JANSEN, Hans J BUTLER, Derek PIROVANO, Walter |
| description | De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. 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 promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%. |
| doi_str_mv | 10.1093/bioinformatics/btq683 |
| format | Article |
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Psychology</topic><topic>Gene Library</topic><topic>General aspects</topic><topic>Genome</topic><topic>Genomics - methods</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. 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| source | Oxford Journals Open Access Collection; MEDLINE; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Algorithms Biological and medical sciences Contig Mapping Fundamental and applied biological sciences. Psychology Gene Library General aspects Genome Genomics - methods Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Sequence Analysis, DNA - methods Software |
| title | Scaffolding pre-assembled contigs using SSPACE |
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