Welcome to our New Website

EdgeBio Icon LogoIf you are reading the full version of this blog you have undoubtedly found you way to our new and improved website. This is just the first of many changes or new offerings we plan to roll out this year in response to wonderful customer feedback. The new layout was designed to allow first-time visitors and repeat users to find information much more quickly than before. The layout is simpler and much more intuitive. Our navigation bars remain constant ( I know, what a novel concept…) so that you can remember where you are and how you got there. Once you get there, you will see quite a bit of new information regarding the different platforms that we run (Ion Torrent PGM, Illuina HiSeq2000 & Life SOLiD). The data generated off of these platforms are available for download. You can also find a ton of information (and some data to boot!) on the different types of sequencing we do, from ChIP-seq to Whole exome sequencing, to Whole transcriptome sequencing to amplicon resequencing, and everything in between.

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$1,000 Genome - Widespread Adoption of NGS?

$1,000 GenomeI attended the Human Genome Meeting last week in Sydney, Australia, due to our involvement with the X Prize. It was my first time at the meeting and I came away very impressed at the level of sequencing being presented during the talks. Many of the talks led off by John McPherson’s talk on Cancer Genomics, and were highlighted by Michael Snyder’s talk on using Omics profiling for assessing disease risk and heath states. Through all of the talks a central theme emerged in my eyes, that the $1,000 genome would lead to widespread adoption of NGS as a clinical diagnostic tool. Much has been written and said about the promise of genomics technology and its impact on personalized medicine. However, that is not the focus of this spot. I would prefer to assess the merits of the premise that the cost alone will lead to rapid adoption sequencing as a clinical assay.

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Microbial Annotation in the Cloud: CloVR and Ion Torrent

At EdgeBio we constantly try to extend the applications and services that we can perform utilizing Ion Torrent sequencing.  Recently we have been involved in some projects with microbial annotation. Microbial Annotation in the CloudBy annotating the results of de novo sequencing with gene predictions researchers can examine the results of the sequencing for biological significance.  With Ion Torrent sequencing the focus is on providing these results quickly and efficiently to our customers.  While there are many tools and options for microbial annotation, one particularly useful and interesting option is CloVR.  CloVR is a tool that packages many commonly used bioinformatics tools into intuitive pipelines.  CloVR is distributed as a virtual machine, allowing users to spin up the environment on a local machine or, even cooler, spin up an instance on Amazon EC2.  Because of its use of cloud computing and its intuitive web interface, CloVR is an attractive tool for many commonly performed bioinformatics tasks.  Pipelines include CloVR-Search that can perform large scale BLAST searches, CloVR-16S for ribosomal RNA sequence analysis, CloVR-metagenomics for taxonomic and functional classification, and CloVR-Microbe that allows for assembly and/or annotation of microbial organisms.  Today I’d like to share our experience using the CloVR-Microbe pipeline for annotation of Ion Torrent data.  Ion Torrent data isn’t yet officially supported, but because 454 data can be used as input to the pipeline, with a little effort Ion Torrent data can be successfully annotated as well.