Difference between revisions of "SEECER"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary= | + | |sw summary=Sequence error correction for RNA-Seq data |
| − | |bio domain=RNA Seq | + | |bio domain=RNA-Seq quantification |
| − | |bio tech=Illumina, 454, | + | |bio method=Sequence error correction, |
| + | |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= | + | |input format=FASTA, FASTQ, |
| − | |output format= | + | |output format=FASTA |
|sw feature=supports multicore processors | |sw feature=supports multicore processors | ||
|language=C | |language=C | ||
}} | }} | ||
| − | |||
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. | 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}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 18:22, 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) | Sequence 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: Sequence error correction for RNA-Seq data
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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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Search for "SEECER" in the SEQanswers forum / BioStar or:
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