SSPACE
Application data |
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Created by | Marten Boetzer and Walter Pirovano |
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Biological application domain(s) | Genomics |
Principal bioinformatics method(s) | Scaffolding |
Technology | Illumina, ABI SOLiD, 454 |
Created at | BaseClear BV (www.baseclear.com) |
Maintained? | Yes |
Input format(s) | FASTA, FASTQ |
Output format(s) | FASTA |
Software features | Scaffold contigs using paired reads. Extension of unmapped reads. Visualisation and tracking of contigs on scaffolds. |
Programming language(s) | Perl |
Operating system(s) | Windows, Linux, Mac OS X |
Summary: Stand-alone scaffolder of pre-assembled contigs using paired-read data.
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Description
Stand-alone scaffolder of pre-assembled contigs using paired-read data.
For example, 454 contigs can be joined into long scaffolds containing many contigs with information from paired end Illumina sequence 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.
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