MapView: visualization of short reads alignment on a desktop computer

A Simple Shortcut to Unsupervised Alignment-Free phylogenetic genome Groupings, even from Unassembled sequencing reads

We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a represe...

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

SUMMARY Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are no...

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

BACKGROUND Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, ow...

Two Web-based Spatial Data Visualization and Mining Systems: Mapcube & Mapview

ZOOM Lite: next-generation sequencing data mapping and visualization software

High-throughput next-generation sequencing technologies pose increasing demands on the efficiency, accuracy and usability of data analysis software. In this article, we present ZOOM Lite, a software for efficient reads mapping and result visualization. With a kernel capable of mapping tens of millions of Illumina or AB SOLiD sequencing reads efficiently and accurately, and an intuitive graphica...