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Wiley-VCH Book, NextGene, Velvet, HeliSphere Technology Center, RDT 1000

Wiley-VCH has published Next Generation Genome Sequencing: Towards Personalized Medicine. The book, which is edited by Michal Janitz, covers commercially available and emerging new sequencing technologies. It costs $200 in the US.

Applied Biosystems said last week that two software tools, from SoftGenetics and the European Bioinformatics Institute, are now available at the company's SOLiD Software Development Community website.
SoftGenetics is providing its NextGene software, which analyzes data from multiple applications generated on next-generation sequencing platforms and enables the assembly, alignment, quality control, and annotation of de novo sequencing data. The EBI has contributed Velvet, a short read de novo assembly tool. In collaboration with EBI, ABI has developed a de novo assembly bioinformatics pipeline that can produce scaffolds up to 50 kilobases long and convert color-space contigs into base-space contigs for easier viewing and analysis.

Helicos BioSciences has launched the HeliSphere Technology Center, a website on which the company shares datasets and bioinformatics tools. The first sample datasets released include whole genome sequences of the microbes Escherichia coli, Staphylococcus aureus, and Rhodobacter sphaeroides. Each sample dataset, containing between six and 12 million aligned reads, was generated from one channel of a 50-channel run on the HeliScope sequencer. Data from additional sequencing projects will be posted on the site on a regular basis.

RainDance Technologies has introduced its instrument, RDT 1000, along with an application for targeted genome sequencing. The RDT 1000 generates picoliter-volume PCR reactions in droplets at a rate of 10 million per hour. According to the company, it can amplify hundreds to thousands of genomic loci with high specificity and uniformity.
The company plans to launch the instrument and application, which are currently in early-access testing, during the first quarter of 2009.

The Scan

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Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.