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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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...Today, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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