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- W2057253402 abstract "Abstract Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k-mers to count. We present a new streaming algorithm for k-mer counting, called DSK (disk streaming of k-mers), which only requires a fixed user-defined amount of memory and disk space. This approach realizes a memory, time and disk trade-off. The multi-set of all k-mers present in the reads is partitioned, and partitions are saved to disk. Then, each partition is separately loaded in memory in a temporary hash table. The k-mer counts are returned by traversing each hash table. Low-abundance k-mers are optionally filtered. DSK is the first approach that is able to count all the 27-mers of a human genome dataset using only 4.0 GB of memory and moderate disk space (160 GB), in 17.9 h. DSK can replace a popular k-mer counting software (Jellyfish) on small-memory servers. Availability: http://minia.genouest.org/dsk Contact: rayan.chikhi@ens-cachan.org" @default.
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- W2057253402 date "2013-01-16" @default.
- W2057253402 modified "2023-10-17" @default.
- W2057253402 title "DSK: <i>k</i>-mer counting with very low memory usage" @default.
- W2057253402 cites W2096128575 @default.
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- W2057253402 doi "https://doi.org/10.1093/bioinformatics/btt020" @default.
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