Analysis - Analysis Engine

Introduction
Recently, sequencing costs have dropped sharply due to increased throughput, simplification, and affordability of second (or even third and fourth) generation sequencing technologies, leading to an explosion of smaller sequencing facilities. However, despite the increased rate of sequence generation, there has not been a commensurate increase in access to computational resources to support high-quality sequence processing and analysis. The Annotation Engine has been effective in providing prokaryotic annotation services to the community for four years, however the analysis needs of researchers now far exceed prokaryotic genome annotation. Therefore we have expanded the analysis pipelines offered in our service to include comparative genomics and transcriptome analysis. We have renamed our service the Analysis Engine. Work is underway to further increase the types of analyses included in the service as well as to increase the interoperability of our tools with other popular bioinformatics tools.

Free Prokaryotic Analysis Engine Services

Whole genome annotation:
Automated structural and functional annotation of genomes using the IGS Prokaryotic Annotation Pipeline (PMID:21677861) and the Manatee visualization tool. Read more.

Comparative genomics:
Automated whole genome comparisons that provide ortholog groups, syntenic regions and visualization of results using Sybil. Read more.

Transcriptome analysis:
Mapping of RNA-Seq reads to a reference genome and differential expression analysis. Read more.

Assembly of genomes with CloVR:
Prepacked assembly pipelines are available as virtual machines with CloVR.

Training workshops are available on many aspects of these analyses, please click here for more information

Custom Analysis
If you have analysis needs beyond what are offered in the free services listed above, please contact us to discuss the needs of your project. We can provide custom analyses (for both prokaryotes and eukaryotes) on a fee-for-service basis.

How to reference use of the IGS Analysis Engine in your publication
We ask that anyone using the IGS Analysis Engine for their work include that information in the Materials and Methods section and to acknowledge us in the Acknowledgements section. Thank You.

We gratefully acknowledge the National Institute of General Medical Sciences for funding this work.