SEECER is a sequencing error correction algorithm for RNA-seq data sets. It takes the raw read sequences produced by a next generation sequencing platform like machines from Illumina or Roche. SEECER removes mismatch and indel errors from the raw reads and significantly improves downstream analysis of the data. Especially if the RNA-Seq data is used to produce a de novo transcriptome assembly, running SEECER can have tremendous impact on the quality of the assembly.


Version 0.1.3 of SEECER is available now.

  • Improved error handling of SEECER pipeline.
  • Update to Jellyfish version 1.1.11. This should fix problems with some of the bigger datasets where the pipeline crashed.

The paper has been published: Probabilistic error correction for RNA sequencing, Nucleic Acids Research (2013).

Version 0.1.2 of SEECER is available now.

  • fixed an issue with processing some FastQ files.

Version 0.1.1 of SEECER is available now.

  • removed warnings to avoid compiler problems on Ubuntu
  • improved scalability because parallelization is now lock-free to support machines with many cores


Hai-Son Le, Marcel H. Schulz, Brenna M. McCauley, Veronica F. Hinman and Ziv Bar-Joseph. Probabilistic error correction for RNA sequencing. Nucleic Acids Research (2013)