Difference between revisions of "Oases"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=De novo transcriptome assembler for very short reads | |sw summary=De novo transcriptome assembler for very short reads | ||
| − | |bio domain= | + | |bio domain=Sequence assembly (de-novo assembly), Transcriptome assembly |
|bio tech=Illumina, ABI SOLiD, 454 | |bio tech=Illumina, ABI SOLiD, 454 | ||
| − | |created by= | + | |created by=Schulz MH, Zerbino DR |
|created at=MPI, EBI | |created at=MPI, EBI | ||
|maintained=Yes | |maintained=Yes | ||
| + | |input format=Fasta, Fasta.gz, Fastq, Fastq.gz, SAM, | ||
| + | |output format=Fasta | ||
| + | |sw feature=supports strand specific and paired-end RNA-seq data sets | ||
|language=C, | |language=C, | ||
|licence=GPLv3, | |licence=GPLv3, | ||
}} | }} | ||
Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | ||
| − | It was developed by Marcel Schulz (MPI for Molecular | + | It was developed by Marcel Schulz (previously MPI for Molecular Genetics, now Lane Center, Carnegie Mellon University) and Daniel Zerbino (at European Bioinformatics Institute (EMBL-EBI), previously at UC Santa Cruz). |
| − | Oases | + | Oases loads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms using the similarities between de Bruijn graphs and splicing graphs. Since version 0.2, Oases contains a merge module that allows to merge different single-k assemblies to improve sensitivity. |
{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 17:08, 19 December 2015
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Application data |
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| Created by | Schulz MH, Zerbino DR |
|---|---|
| Biological application domain(s) | Sequence assembly (de-novo assembly), Transcriptome assembly |
| Technology | Illumina, ABI SOLiD, 454 |
| Created at | MPI, EBI |
| Maintained? | Yes |
| Input format(s) | Fasta, Fasta.gz, Fastq, Fastq.gz, SAM |
| Output format(s) | Fasta |
| Software features | supports strand specific and paired-end RNA-seq data sets |
| Programming language(s) | C |
| Licence | GPLv3 |
Summary: De novo transcriptome assembler for very short reads
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Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (previously MPI for Molecular Genetics, now Lane Center, Carnegie Mellon University) and Daniel Zerbino (at European Bioinformatics Institute (EMBL-EBI), previously at UC Santa Cruz).
Oases loads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms using the similarities between de Bruijn graphs and splicing graphs. Since version 0.2, Oases contains a merge module that allows to merge different single-k assemblies to improve sensitivity.
Links
References
To add a reference for Oases, enter the PubMed ID in the field below and click 'Add'.
Search for "Oases" in the SEQanswers forum / BioStar or:
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