Correcting errors in short reads by multiple alignments

Correcting errors in short reads by multiple alignments

MOTIVATION Current sequencing technologies produce a large number of erroneous reads. The sequencing errors present a major challenge in utilizing the data in de novo sequencing projects as assemblers have difficulties in dealing with errors. RESULTS We present Coral which corrects sequencing errors by forming multiple alignments. Unlike previous tools for error correction, Coral can utilize ...

CoLoRMap: Correcting Long Reads by Mapping short reads

MOTIVATION Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are charac...

Aligning short reads to reference alignments and trees

MOTIVATION Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignmen...

Sequences, Reads, Alignments, and Ranges

Correcting multiple design errors in digital VLSI circuits

Andreas G.Veneris University of Illinois at Urbana-Champaign Department of Computer Science e-mail: [email protected] Ibrahim N.Hajj University of Illinois at Urbana-Champaign Department of Electrical and Computer Engineering e-mail: [email protected] Abstract With the increase in the complexity of VLSI circuit design, logic design errors can occur during the synthesis process. In...