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Partek® Flow® Now Available in Illumina’s BaseSpace Apps

Published: Tuesday, November 06, 2012
Last Updated: Tuesday, November 06, 2012
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Partek® announced it has added Partek® Flow® to Illumina’s BaseSpace Apps, Illumina’s dedicated applications store and informatics community dedicated to advancing genomic analysis.

Partek Flow is utilized for multiple next generation sequencing applications including RNA-Seq, small RNA-Seq, exome, and targeted sequencing. It provides a single web-based environment to carry out multiple tasks, which can be executed an unlimited number of times on an unlimited number of samples.

When asked about the broad and diverse tool set contained within Partek Flow for researchers, Tom Downey, president of Partek stated, “When designing our software, we insisted on diverse functionality giving users multiple tools to interact with their data. Questions that biologists are exploring cannot be answered in a single step process. Rather, we want to support their desire to directly interact with their data and Partek Flow provides an interactive ecosystem to do that. Alignment, variant and indel detection, powerful statistical algorithms, identification of differentially expressed genes, chromosome viewer, and visualization tools such as 3D PCA, charts, and graphs that delve deeper into data quality are all tools at the researcher’s disposal.” Downey went on to say, “With Partek Flow, we have advanced our goal of bringing down the barrier to analysis to enable more biologists and scientific researchers to ask the relevant biological questions about their data directly.”

With the Partek Flow app, which analyzes the data specified by the user in BaseSpace, users can carry out both primary and secondary analysis with a single tool, saving time by not having to import and export various data formats through different applications. With a single application a user can take both unaligned or already aligned data and carry out multiple downstream analysis steps for multiple sequencing applications. The interactive visualizations enable users to ask a multitude of biological questions to extract meaning from their data. For example in the RNA-Seq workflow, the data can be aligned, transcripts quantified, and differentially expressed genes detected resulting in an interactive table of genes. Researchers can then drill down and visualize the summarized transcript levels as well as the individual sequence. Variant analysis can also be carried out to interrogate allele specific expression and visualized.

Included in Partek Flow are publicly available statistical algorithms as well as those developed and optimized by Partek such as their Gene Specific Algorithm for the detection of differentially expressed genes, which won the Illumina iDEA Challenge award for most creative algorithm. Partek is pleased to be the only commercial provider for RNA-Seq analysis on BaseSpace today.

Informatics solutions available through BaseSpace Apps will allow customers to utilize the tools from a growing community of academic, commercial, and open source providers. To demonstrate the utility of this rapidly growing toolset, BaseSpace customers will have free access to all of the BaseSpace Apps until January 1, 2013.


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