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Downloads and Upgrades: ContEst, SMRT Analysis 2.1, PEAKS Studio 7, and more


Appistry has added ContEst, a new tool for estimating cross-contamination in NGS tumor/normal samples, to its Cancer Genome Analysis suite. According to the company, ContEst, which was developed by researchers at the Broad Institute, will provide users with enhanced specificity by eliminating false positives called due to sample contamination.

The UCSC Genome Bioinformatics group has released a new track — a 100 species alignment on for the human genome browser.

This new conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods — phastCons and phyloP from the PHAST package. The update adds 40 more
species to the existing 60 species track on the mm10 mouse browser.

Pacific Biosciences has released SMRT Analysis 2.1, the latest version of the company's open source sequence analysis software.

The release includes bug fixes, enhanced bar coding support, consensus calling on diploid samples, a beta version of the BridgeMapper visualization tool for assembly Q/C analysis, and more.

DNAnexus has released a dataset of genetic variants culled from analyzing 80 terabytes of genomic data from the 1000 Genomes Project. The company worked with researchers at Stanford University to generate the data.

Bioinformatics Solutions has released PEAKS Studio 7, the latest version of its software for proteomics mass spectrometry data analysis.

Among other updates, this release offers faster protein identification and an automatic validation approach for de novo sequencing.

Ensembl release 74 is available here.

The release includes updated patches for the human assembly and updated dbSNP 138 data for humans. It also include three new species — sheep (Ovis aries), cave fish (Astyanax mexicanus) and, spotted gar (Lepisosteus oculatus) — among other updates.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.