SSPACE
|
Application data |
|
| Created by | Marten Boetzer and Walter Pirovano |
|---|---|
| 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.
"Error: no local variable "counter" was set." is not a number.
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.
Links
References
To add a reference for SSPACE, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "SSPACE" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
