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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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
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05-06-2024, 07:48 AM -
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