Fiona: A parallel and automatic strategy for read error correction

Abstract

Fiona is a tool for the automatic correction of sequencing errors in reads produced by high throughput sequencing experiments. It uses an efficient implementation of suffix arrays to detect read overlaps with different seed lengths in parallel. Fiona was compared on several real datasets to state-of-the-art methods and  showed overall superior correction accuracy. It was also among the fastest. Additionaly Fiona embarks unique characteristics which makes it a good choice over existing programs:

  • No parameters to set for the user. You just need to know the length of the genome!
  • Correction of both substitution and indel errors.
  • Optimal correction over a range of seed values.
  • Multicore-Parallelization using OpenMP.
  • Efficient, memory-saving implementation.

Links

Please Cite

Schulz M.H., Weese D., Holtgrewe M., Dimitrova V., Niu S., Reinert K., & Richard H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics (2014) 30 (17): i356-i363

Contact

For questions, comments, or suggestions please contact:

Marcel Schulz
maschulz@andrew.cmu.edu