RECKONER: read error corrector based on KMC

RECKONER: read error corrector based on KMC

Summary Presence of sequencing errors in data produced by next-generation sequencers affects quality of downstream analyzes. Accuracy of them can be improved by performing error correction of sequencing reads. We introduce a new correction algorithm capable of processing eukaryotic close to 500 Mbp-genome-size, high error-rated data using less than 4 GB of RAM in about 35 min on 16-core compute...

QuorUM: An Error Corrector for Illumina Reads

MOTIVATION Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous k...

An elective in KMC.

Kmc Modeling of Helium

The effect of helium in iron is an important issue in nuclear systems, as iron and iron alloys (steels) are the primary materials used for structural elements. Helium is known to cause embrittlement and decrease fatigue life, as well as aid creep and promote swelling. These effects can significantly alter the mechanical properties of the reactor materials, and generally lead to early failure an...

SHREC: a short-read error correction method

MOTIVATION Second-generation sequencing technologies produce a massive amount of short reads in a single experiment. However, sequencing errors can cause major problems when using this approach for de novo sequencing applications. Moreover, existing error correction methods have been designed and optimized for shotgun sequencing. Therefore, there is an urgent need for the design of fast and acc...