Difference between revisions of "SEECER"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Error correction for RNA-Seq data | |sw summary=Error correction for RNA-Seq data | ||
| − | |bio domain=RNA Seq quantification | + | |bio domain=RNA-Seq quantification |
| − | |bio method=Error correction, | + | |bio method=Error correction, |
|bio tech=Illumina, 454, Ion Torrent, PacBio, | |bio tech=Illumina, 454, Ion Torrent, PacBio, | ||
|created by=Le H, Schulz MH, Bar-Joseph Z | |created by=Le H, Schulz MH, Bar-Joseph Z | ||
Revision as of 16:52, 2 December 2015
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Application data |
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| Created by | Le H, Schulz MH, Bar-Joseph Z |
|---|---|
| Biological application domain(s) | RNA-Seq quantification |
| Principal bioinformatics method(s) | Error correction |
| Technology | Illumina, 454, Ion Torrent, PacBio |
| Created at | Carnegie Mellon University |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | FASTA |
| Software features | supports multicore processors |
| Programming language(s) | C |
Summary: Error correction for RNA-Seq data
"Error: no local variable "counter" was set." is not a number.
SEECER is an error correction method that removes errors that are introduced during sequencing. Mismatches, insertion or deletions are removed by creating multiple alignments of reads and building HMMs that are used to decide which reads are be corrected. In the provided reference it is shown that error correction with SEECER improves the downstream analysis, especially RNA de novo assembly.
Links
References
To add a reference for SEECER, enter the PubMed ID in the field below and click 'Add'.
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