Amin Allam
Lecturer (Doctor), Computer Science Department, Faculty of Computers and Artificial Intelligence
a.allam@fci-cu.edu.eg (email)
Karect: Accurate Correction of Substitution, Insertion and Deletion Errors for Next-generation Sequencing Data
I implemented the complete efficient system for "Karect". Karect is a novel error correction technique for next-generation sequencing, based on multiple alignment, supporting substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the sequenced genome. Experiments with data from Illumina, 454 FLX and Ion Torrent sequencing machines demonstrate that Karect is more accurate than previous methods, both in terms of correcting individual-bases errors (upto 10% increase in accuracy gain), and post de novo assembly quality (upto 10% increase in NGA50). Karect has been published in the Bioinformatics journal, a top-ranked journal in the bioinformatics area. Karect is available at here.