Difference between revisions of "SEECER"
| Line 2: | Line 2: | ||
|sw summary=Error correction for RNA-Seq data | |sw summary=Error correction for RNA-Seq data | ||
|bio domain=RNA Seq analysis | |bio domain=RNA Seq analysis | ||
| − | |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 | ||
|created at=Carnegie Mellon University | |created at=Carnegie Mellon University | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=FASTA, FASTQ, | + | |input format=FASTA, FASTQ, |
| − | |output format= | + | |output format=FASTA |
|sw feature=supports multicore processors | |sw feature=supports multicore processors | ||
|language=C | |language=C | ||
Revision as of 00:17, 11 May 2013
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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 analysis |
| 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
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