Decoding Breast Cancer using Strand NGS DNA Variant analysis

One of the most dreaded diseases mankind has faced in recent times is cancer. Because of high morbidity and mortality rates that cancer brings it is a fearsome disease. When we hear about cancer no one believes that it can happen to them or to anyone else close. But the reality is far from this. … Continue reading “Decoding Breast Cancer using Strand NGS DNA Variant analysis”

The tyranny of large numbers: mutations in breast cancer

What’s in a number? Small numbers are roguish capsules of triple meaning. The number 7 is the date you were married; it’s the exact number of teaspoons of sugar in a halwa recipe your mom sent you; it’s the age of your eldest son on his next birthday. As we get older, we become acquainted … Continue reading “The tyranny of large numbers: mutations in breast cancer”

Accuracy puts the there in speed: DNA-Seq stuff!

In certain circles, asking why speed is good is tantamount to heresy. I once submitted a paper with the phrase “computational performance is not an explicit goal of this work” in the abstract. It was rejected; in his explanatory note, the reviewer had said that my approach was “unlikely to yield great speedups,” and that … Continue reading “Accuracy puts the there in speed: DNA-Seq stuff!”

It’s pronounced three dot oh

Getting things to “just work” is hard. Getting them to just work and be good is harder. With StrandNGS 3.0, we believe we’ve done both. A quarter year’s labour of love, three dot oh feels different because it is different; it feels good because it is. RNA alignment is faster. If you’re using transcriptome + genome alignment, you … Continue reading “It’s pronounced three dot oh”

Rare diseases: or, what happens when backups fail

Ploidy is a funny old Greek word for a modern, almost modish concept: data backups. Ploidy is the number of copies of an organism’s DNA. Certain kinds of algae, for instance, don’t buy into backups; they’re haploid, and contain only a single copy of DNA. Plants, on the other hand, are polyploidal; paranoiacs of the … Continue reading “Rare diseases: or, what happens when backups fail”

The clinical workflow, retinoblastoma and split alignment

    Retinoblastoma is an “oma” named for its surface effect, its “presentation”:  it’s a cancer that attacks the eye. Worse, because 80% of retinoblastoma diagnoses occur before the age of 3, it’s a cancer that attacks the eyes—almost exclusively—of little children. Retinoblastoma is a “good cancer”: 90% of all RB cases survive into adulthood. … Continue reading “The clinical workflow, retinoblastoma and split alignment”

Reduce the SNP annotation time by up to 95%

Explore the new script ‘Create Targeted VAL’ in Strand NGS for creating subset of dbSNP database with target regions of interest and run your analysis. This feature reduces your SNP annotation time by up to 95% depending on the target regions of interest. Strand NGS v2.7 has more exciting features. Listed below are few:

Strand NGS v2.7 released

We are excited to share the release of Strand NGS v2.7. This new version comes with several exciting features and enhancements. Listed below are few major enhancements:

Review of selected publications citing Strand NGS

In 2015, we brought in many new features and improvements based on your requirements and feedback. We expanded the Strand NGS epigenomics toolkit by adding the MeDIP-Seq workflow in the v2.5 release. We also added new features like the alignment workflow and SV detection for split reads (watch the webinar), a browser-based copy number variation (CNV) view … Continue reading “Review of selected publications citing Strand NGS”

Webinar on Strand NGS Pipeline Manager for streamlining large scale analysis

This webinar, will highlight the Strand NGS Pipeline Manager feature. In this webinar, you will learn how to customize pipelines and share them with other Strand NGS users. This webinar will give a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and … Continue reading “Webinar on Strand NGS Pipeline Manager for streamlining large scale analysis”