Greetings, we started the assembly of a small bacterial genome from 1 SMRT PacBio run last night on Amazon EC2 services using HGAP. Just wondering if anyone else out there has tried this, and could provide a time estimate for assembly. There were 87000 post-filtered post filter polymerase read length ~4700bp. The tutorial I watched used optimized E. coli reads with several SMRT cells on a multi-CPU computer, they said it would take ~few hours...
-
-
What size instance are you using? are you using the HGAP.1, or HGAP.2 protocol? Viewing the log, top right on the job page will give you a % complete estimate. Also viewing ./common/userdate/jobs/<job id>/workflow/Workflow.summary.html will give you a detailed view of the tasks that have complete, and what is remaining to be ran.
-
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...Yesterday, 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