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Downloads and Upgrades: BaseSpace Apps, Geneious R6, Ion Reporter v1.2, and more.

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Several bioinformatics companies who signed on to Illumina’s BaseSpace program released their applications for the cloud infrastructure this week at the American Society of Human Genetics conference.

Partek launched the Partek Flow app, which provides tools for analyzing RNA-seq and small RNA-seq data as well as from exome and targeted sequencing. It includes algorithms for sequence alignment, variant and indel detection, identification of differentially expressed genes, and visualization tools among other capabilities.

Meanwhile, Golden Helix added GenomeBrowse to the BaseSpace store. The app provides visualization tools for DNA and RNA sequence data. It also provides a cloud-based repository of public annotations from dbSNP, 1000 Genomes, NHLBI 6500 Exomes, UCSC Known Genes, Ensembl, the Online Mendelian Inheritance in Man catalog, and others.

DNAStar added a de novo bacterial genome assembly app to the store, which supports rapid assembly of Illumina sequence reads using DNAStar’s SeqMan NGen program and patented assembly algorithms. The app helps users assemble paired-end reads from Illumina HiSeq or MiSeq instruments directly in BaseSpace and visualize the results in a genome browser from within BaseSpace. In addition, users of the app will also receive a free trial version of the company’s Lasergene software to further analyze their results.

Finally, Biomatters added its Molecular Profiler app — a cloud-based genome browser — to the BaseSpace store

BaseSpace customers will have free access to all of the BaseSpace Apps until Jan. 1, 2013.


Biomatters has also launched Geneious R6, the latest version of its DNA and protein analysis, alignment, and assembly software.

The release offers improved visualization tools, new thermodynamic calculations that provide better stats on primers, and automatic plasmid annotation among other updates.


Life Technologies has released version 1.2 of its Ion Reporter software

The release lets users process genomic data using predefined workflows optimized for specific sequencing panels and the most popular experimental designs, such as an oncology tumor-normal workflow and an inherited disease workflow. It also includes a new collaborations feature that lets users share samples, analyses, and results. Finally, the software has been integrated with the Ingenuity Variant Analysis workflow, allowing users to leverage the Ingenuity Knowledgebase to identify biologically relevant variants.

Both Ion Reporter 1.2 and the Ingenuity Variant Analysis workflow are available free of charge until the end of 2012.


CLC Bio and BioQL have released the MedQL Variant Prioritizer plugin for the CLC Genomics Workbench.

The plugin connects the genomics workbench with MedQL’s online database, allowing users to prioritize list of variants in gene regions based on their degree of association with a given phenotype. The database contains more than 20 million articles from Medline, indexed using a dictionary of nearly 300,000 terms from ontologies such as the HUGO Gene Nomenclature Committee, the Human Disease Ontology, and OMIM.

The initial release of the MedQL plugin is a free version, which can process a maximum of 10 queries of 50 genes per day. Later this year, a premium plugin without these restrictions will be made available for download directly from CLC Bio’s website.


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