Tweet
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 .
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment