Kmer

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A kmer or k-mer is a short DNA sequence consisting of a fixed number (K) of bases. The value of k is usually divisible by 4 so that a kmer can fit compactly into a basevector object. Typical values include 12, 20, 24, 36, and 48; kmers of these sizes are referred to as 12-mers, 20-mers, and so forth.

Kmers are essential to pre-processing of reads and contigs. A typical procedure is to cut a contig into a series of overlapping kmers; each kmer overlaps with its neighbors in all but one base as they step through the sequence. This is how lookup tables are generated.

Arachne objects that handle kmers include kmer_with_count and KmerRecord.

Modules that input or output kmers include the lookup table modules, as well as CompareKmers, CountKmers, KmerKonsensus, FindGenomicKmers, FastbToStandardKmers, and FixLocationsWithKmers.

A mutmer is a kmer of variable ("mutable") length K. Certain algorithms involving kmers have been adapted to use mutmers within a range of lengths.

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