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 should see a 30-50% increase in speed. If you’re using transcriptome-only alignment, that increase should be closer to twofold.
DNA-Seq is faster and more accurate. We now call variants from whole exome and whole genome samples about twice as fast as the GATK best-practices workflow, while achieving comparable precision and recall rates. If you want to get to variants fast, we have a one-shot pipeline just for you. If you care about the details—and who doesn’t?—we have a white paper, available for download from our website.
ChIP-Seq now has Transcription Start Site (TSS) plots, great for when you need coverage profiles near a TSS. TSS plots support multiple samples, and work across multiple groupings of genes.
HGVS, the industry-standard for describing human variation, is in place. Strand NGS supports cDNA, Protein, and Genomic HGVS notation, each available by default in the SNP effect analysis workflow.
There’s a whole host of other changes, ranging from under-the-hood tweaks to serious—and seriously geeky—conceptual changes. Strand NGS is so vast that you may never see any of these; but you might, in your day-to-day, sense their presence behind the generally smooth and rich experience that Strand NGS provides.
We hope you enjoy using three dot oh. We enjoyed making it.
For detailed information, do register for our upcoming webinar on 26th April 2017.