New and Updated BaseSpace Apps

It’s been an exciting last 30 days for App releases. At the end of February we released v1.1 of the TruSeq Long-Read Assembly and the TruSeq Phasing Analysis Apps.


TruSeq Long-Read Assembly v1.1

TruSeq Phasing Analysis Apps v1.1

These updates were mainly to improve the performance of the Apps and to fix a few minor bugs. Detailed information can be found in the customer release note.

We also released v2.1 of the Isaac Enrichment and BWA Enrichment Apps.

Isaac Enrichment v2.1

BWA Enrichment v2.1

These updates allow the Apps to take advantage of the multi-launch feature available in the BaseSpace platform. Users can now analyze up to 96 samples in parallel across multiple nodes dramatically reducing the time to answer. 96 samples can now be analyzed in as little as 2 hours on a 50x exome. Detailed information can be found in the customer release note.

We also published a handfull of new 3rd Party Apps.

The GENIUS Metagenomics: Know Now App from COSMOSID was released. The release of the App was discussed in GenomeWeb. The GENIUS® Metagenomics application uses CosmosID’s curated genome database and high performance algorithms to provide rapid, accurate, and actionable bacterial identification at the species, subspecies, and/or strain level. You can explore the App for free with their limited time free trial offer (through April 3, 2015).

Genius Metagenomics: Know Now

The MetaPhlAn App from the Huttenhower Lab at the Harvard School of Public Health was published. Like The GENIUS® Metagenomics application the MetaPhlAn App adds to our growing suite of tools for microbiology data analysis. MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.


The EDGC Annotator v1.0 App from EONE-DIAGNOMICS Genome Center was published. EDGC Annotator annotates human variants by providing information about cancer related variants, genomic regions, allele frequency data, clinical knowledge and insights using ClinVar, OMIM, COSMIC, 1000 Genomes Project allele frequencies, dbSNP and VEP(Variant Effect Predictor) database.

EDGC Annotator v1.0

The RNA-Seq Translator v1.0 App from Yale University was published. The App compliments our suite of Apps for the OneOmics project. The App consumes the output of the Cufflinks Assembly and DE App and converts the differential expressed genes to create a protein reference with which to search spectra obtained from a mass-spectrometry experiment.

RNA-Seq Translator v1.0

Finally we published an updated version 3.5 of the SPAdes Genome Assembler App from the Algorithmic Biology Lab. SPAdes is a best in class de novo assembler for assembly of small genomes. This update includes improved support for Nextera® Mate Pair Libraries which allows users to generate large continuous high quality assemblies. Users can also mix multiple libraries in a single assembly

SPAdes Genome Assembler 3.5

We are excited about these new and updated Apps and the continued maturity of the BaseSpace platform. We now have around 60 Apps on BaseSpace covering many of the NGS analysis needs.  We look forward to bringing more functionality in the days to come.

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