I thought the new "scaffold" option in Newbler might do something interesting with my shotgun data even though I thought this term was previously only discussed in relation to paired-end data. Anyway, I have tried doing a de novo assembly of shotgun data both with and without the scaffold option selected. It seems that the scaffold output is identical to the largest contigs (of course there is variation depending upon scaffold and large contig length cutoffs). Is this normal or should I have expected anything different?
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...Today, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment