Fast and accurate DNASeq variant calling workflow composed of LUSH toolkit.

Background: Whole genome sequencing (WGS) is becoming increasingly prevalent for molecular diagnosis, staging and prognosis because of its declining costs and the ability to detect nearly all genes associated with a patient's disease. The currently widely accepted variant calling pipeline, GATK, is limited in terms of its computational speed and efficiency, which cannot meet the growing analysis needs.

Results: Here, we propose a fast and accurate DNASeq variant calling workflow that is purely composed of tools from LUSH toolkit.

GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.

Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing owing to its unbiasedness and substantially reduced costs. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in dry-lab step of mNGS test. However, clinical practices of the testing technology are hampered by the challenge of classifying sequences within a clinically relevant timeframe.

Whole-genome and Transcriptome Sequencing of Prostate Cancer Identify New Genetic Alterations Driving Disease Progression.

Background: Global disparities in prostate cancer (PCa) incidence highlight the urgent need to identify genomic abnormalities in prostate tumors in different ethnic populations including Asian men.

Objective: To systematically explore the genomic complexity and define disease-driven genetic alterations in PCa.

Design, Setting, And Participants: The study sequenced whole-genome and transcriptome of tumor-benign paired tissues from 65 treatment-naive Chinese PCa patients.

SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.

Motivation: RNA-Seq provides a powerful approach to carry out ab initio investigation of fusion transcripts representing critical translocation and post-transcriptional events that recode hereditary information. Most of the existing computational fusion detection tools are challenged by the issues of accuracy and how to handle multiple mappings.

Results: We present a novel tool SOAPfusion for fusion discovery with paired-end RNA-Seq reads.

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data.

RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice.