Oases
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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.
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