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.
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Nucleic Acids Res. 2013 May 1;41(10):e109. doi: 10.1093/nar/gkt215
Probabilistic error correction for RNA sequencing.
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.