Lighter and Rcorrector: Tools for Next Generation Sequencing Error Correction

Next generation sequencing (NGS) has tremendously accelerated the pace at which new genomes are being produced. While abundant, reads produced by NGS platforms often contain low-rate sequencing errors. Errors in DNA reads can complicate genome assembly, while errors in RNA-seq reads can lead to fragmentation of gene assemblies or may cause some splice variants to be missed. Error correction of NGS reads can significantly improve the quality of assembly, and ultimately of downstream functional analyses. We developed two software tools, Lighter and Rcorrector, to correct sequencing errors in short DNA and RNA reads produced with Illumina instruments. Both tools employ a k-mer spectrum approach, converting low frequency k-mers in a read into high frequency ones, taking into account characteristics of the data. The DNA read error corrector, Lighter uses a sampling method implemented with two Bloom filters to determine the set of all high-frequency k-mers that are trusted to be error-free. The RNA read corrector, Rcorrector, employs a de Bruijn graph to trace the most likely path, or transcript of origin, for each read. Both tools are fast and accurate, and can fit in the memory of most desktop machines. In applications, Lighter and Rcorrector lead to better genome and transcript assemblies, and therefore will contribute effectively to improving the assembly and annotation of plant and animal genomes.
Availability: https://github.com/mourisl/{Lighter,Rcorrector}.
Funding: NSF IIS-1349906 to BL; NSF IOS-1339134 and ABI-1356078 to LF.