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Note: new posts have moved to http://bcb.io/ Please look there for the latest updates and comments Improvements in next-generation sequencing technology are leading to ever increasing amounts of sequencing data. With this additional throughput comes the demand for algorithms and approaches that can easily scale. Hadoop offers an open source framework for batch processing large files. This post des
Note: new posts have moved to http://bcb.io/ Please look there for the latest updates and comments Next generation sequencing technologies like Illumina, SOLiD and 454 have provided core facilities with the ability to produce large amounts of sequence data. Along with this increased output comes the challenge of managing requests and samples, tracking sequencing runs, and automating downstream ana
For CouchDB, I initially reported large numbers which were improved dramatically with some small tweaks. With a naive loading strategy, times were in the range of 22 hours with large 6G files. Thanks to tips from Chris and Paul in the comments, the loading script was modified to use bulk loading. With this change, loading times and file sizes are in the range of the other stores and the new times
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