Oases | Tool name | Oases |
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| URL | http://www.ebi.ac.uk/~zerbino/oases/ |
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| Important features | 1. 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.
2. Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called loci.
3. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms. |
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| Citations | Schulz M, Zerbino D: Oases - De novo transcriptome assembler for very short reads.Tech. rep., MPI for Molecular Genomics, European Bioinformatics Institute (EMBL-EBI), UC Santa Cruz 2010. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 96 |
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| Comments | |
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| Function | RNA seq alignment, Transcriptome assembler |
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| Category | Downloadable |
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| License | GNU GPL V3 |
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| Status | |
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| Input file format | |
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| Output file format | Fasta |
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| Operating system | 64bit Linux-compatible |
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| Operating language | C |
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| Platform | Illumina/Solexa, ABI SOLiD, Roche 454 |
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| Maintained by | |
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| Downloadable file format | |
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| Submission file format | |
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