Recount: expectation maximization based error correction tool for next generation sequencing data.

Recount: Expectation Maximization Based Error Correction Tool for next Generation Sequencing Data

Algorithms for Viral Population Analysis

The genetic structure of an intra-host viral population has an effect on many clinically important phenotypic traits such as escape from vaccine induced immunity, virulence, and response to antiviral therapies. Next-generation sequencing provides read-coverage sufficient for genomic reconstruction of a heterogeneous, yet highly similar, viral population; and more specifically, for the detection...

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

MOTIVATION Next-generation sequencing presents several statistical challenges, with one of the most fundamental being determining an individual's genotype from multiple aligned short read sequences at a position. Some simple approaches for genotype calling apply fixed filters, such as calling a heterozygote if more than a specified percentage of the reads have variant nucleotide calls. Other ge...

A survey of error-correction methods for next-generation sequencing

UNLABELLED Error Correction is important for most next-generation sequencing applications because highly accurate sequenced reads will likely lead to higher quality results. Many techniques for error correction of sequencing data from next-gen platforms have been developed in the recent years. However, compared with the fast development of sequencing technologies, there is a lack of standardize...

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing

MOTIVATION Next-generation DNA sequencing platforms are becoming increasingly cost-effective and capable of providing enormous number of reads in a relatively short time. However, their accuracy and read lengths are still lagging behind those of conventional Sanger sequencing method. Performance of next-generation sequencing platforms is fundamentally limited by various imperfections in the seq...