UniversalMer2

UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence.

Features

Counting k-mers with multiple k's value at once.
Counting 1-mers to kmax specified by user.
Counting large k-mers in practical time
Support k limit up to any sizes
Finding maximum length of repeat patterns
Support DNA sequences, RNA sequences, and proteins sequences.
Practical running time and memory usage
Show spectrum of 1-mers to kmax-mers within seconds
Dumping 1-mers to kmax-mers patterns within seconds
Enable config minimum frequency

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