SRA Toolkit: the SRA database at your fingertips


The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems.

Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.

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The Tasmanian Devil and Cancer as an Infectious Disease: Analysis of transcriptome data


The Tasmanian devil (Sarcophilus harrisii), the last remaining large marsupial carnivore, now faces extinction because of a strange and deadly infection: a transmissible cancer known as Devil Facial Tumor Disease.  These tumor infections are apparently passed to other devils through bites during mating or during squabbles over carrion when devils gather to feed. In this unusual situation, the cancer cells themselves are the infectious agent.

The failure of devil immune systems to recognize and destroy the foreign tumor cells may be related to a decline in genetic diversity and may serve as a warning about the vulnerability of species with reduced gene pools.  The advent of next-generation sequencing has provided an unprecedented opportunity to track the spread and identify the origin of this unusual zoonosis, as well as to examine the population structure of an endangered mammal and generate a complete genome sequence for this unique marsupial.

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