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A simple management scheme is employed to permit efficient use of main memory.
We present an extension in memory hierarchy, hard disk and main memory, which has as objective to reduce the use of main memory, as well as reducing the page faults, caused by the use of swap.
However, for lower values of support-in this case, less than 1%-MR-Radix algorithm begins to show a lower use of main memory.
To handle large targets without excessive use of main memory, we implement two reporting strategies.
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Our greedy variant using 9 GB of main memory is 2-3 times as fast as the best known variant.
Additionally, efficient external memory (disk-based) BWT construction algorithms have been developed that allow the construction of the FM-index for very large datasets while using a limited amount of main memory (Dementiev et al., 2008; Ferragina et al., 2010).
As this resource is typically cheaper than primary memory, many operating systems are able to use it as an extension of main memory, to temporarily swap out unused memory state.
The whole analysis on 30 million mapped reads (970 million bases) and 3.6 million array features was done using Mayday running with 4GB of main memory.
During the tests we collected the maximum amount of main memory used by the algorithms.
Reanalysis of their data, a comparison of 246 million Illumina reads with the KEGG database (Kanehisa and Goto, 2000), takes ∼2 h on a single workstation (64 cores, 512 GB of main memory) using PAUDA, reproducing the main result of the article.
Although Redis has persistent ability using RDB and AOF, its maximum capacity is limited by the size of main memory.
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