Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the
full catalogue of transcripts and their variations. Recent advances in sequencing …

There has been an exponential growth in the performance and output of sequencing
technologies (omics data) with full genome sequencing now producing gigabases of reads …

Characterizing the errors generated by common high-throughput sequencing platforms and
telling true genetic variation from technical artefacts are two interdependent steps, essential …

We introduce Quake, a program to detect and correct errors in DNA sequencing reads.
Using a maximum likelihood approach incorporating quality values and nucleotide specific …

As the computer industry retools to leverage massively parallel graphics processing units
(GPUs), this book is designed to meet the needs of working software developers who need …

Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids
counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k …

Background Counting k-mers (substrings of length k in DNA sequence data) is an essential
component of many methods in bioinformatics, including for genome and transcriptome …

Motivation: The imperfect sequence data produced by next-generation sequencing
technologies have motivated the development of a number of short-read error correctors in …

The advent of next-generation sequencing technologies is accompanied with the
development of many whole-genome sequence assembly methods and software, especially …

Deep sequencing has enabled the investigation of a wide range of environmental microbial
ecosystems, but the high memory requirements for de novo assembly of short-read shotgun …