The biobambam package contains a tool called bammarkduplicates. It produces results which should be quite similar to those of Picard's MarkDuplicates tool while avoiding the sometimes high memory requirements of the Java implementation. The source code is available on github at https://github.com/gt1/biobambam, binaries for some versions of Linux are at ftp://ftp.sanger.ac.uk/pub/users/gt1/biobambam and also on launchpad https://launchpad.net/biobambam . It was developed at the Sanger Institute because the Java tool failed with out of memory type errors for a number of (at least locally high depth) BAM files, which required manual intervention (rerunning compute jobs with higher memory settings, which blocks otherwise free CPU cores because a single one is using all the RAM). If someone is interested in the algorithmic background, there is a preprint at http://arxiv.org/abs/1306.0836 .
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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...10-30-2026, 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
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