uc-echo

Summary A reference-free error correction algorithm for short read DNA sequencing technologies. Reference Wei-Chun Kao, Andrew H. Chan, and Y. S. Song. ECHO: A reference-free short-read error correction algorithm. Genome Research, Genome Research, 21:1181--1192, 2011. Abstract Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters in the assumed model and estimates error characteristics specific to each sequencing run, while maintaining a running time that is