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New Products: Agilent's 2200 TapeStation, New Software from BGI, MIT/Harvard's CummeRbund, and More


Agilent Technologies has launched the Agilent 2200 TapeStation to automate next-generation sequencing sample and library quality control. The benchtop instrument comes with prepackaged, ready-to-use ScreenTape consumables and is compatible with 16-tube strip vials and 96-well plates.

Chinese genome center BGI has released several new or updated bioinformatics applications, pipelines, and software tools.

They include an updated SOAP package, available here, with SOAP3, a short read aligner; SOAPindel, an indel finder; SAPfusion, a gene fusion detector; SOAPsplice, a splice-junction detector; SOAPdenovo-Trans, a de novo transcriptome assembler; and Metacluster 4.0, a binning solving tool for metagenomics.

Also available are cloud-based analysis software tools for next-gen data analysis, such as GAMA to estimate allele frequency and GSNP for SNP detection; and Adam to sort and remove duplicate reads. In addition, BGI released Hecate 2 and Gaea 2, updated versions of de novo assembly and resequencing analysis tools.

BGI has also launched GigaDB, a publicly available database that houses large-scale genomic datasets from a variety of organisms, including E. coli, foxtail millet, potato, Chinese cabbage, cucumber, pigeonpea, sorghum, ants, roundworm, naked mole rat, sheep, silkworm, Tibetan antelope, and human. Each dataset is assigned a digital object identifier. GigaDB is affiliated with GigaScience, a new research journal published by BGI and BioMed Central.

The computational biology group at MIT's computer science and artificial intelligence laboratory and the Rinn Lab at the Harvard University department of stem cells and regenerative medicine have released CummeRbund, an R/Bioconductor package that simplifies the organization, access, exploration, and visualization of the various output files of a Cuffdiff differential expression analysis. The software is freely available under the OSI approved Artistic License 2.0 and can be downloaded here.

In addition, CummeRbund has been included as part of the new R/Bioconductor v2.9 release and can be installed in a similar manner to standard Bioconductor packages.

Genedata has released Genedata Expressionist 7.0 for Genomic Profiling. The system simultaneously analyzes transcriptomics, copy number variation, variant, and DNA methylation data. It includes a genome browser that can visualize terabytes of data and provide real-time feedback at every processing step.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.