kmerfreq¶
kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and reference genome data is also applicable. The forward and reverse strand of a k-mer are taken as the same k-mer, and only the kmer strand with smaller bit-value is used to represent the kmer. It adopts a 16-bit integer with max value 65535 to store the frequency value of a unique K-mer, and any K-mer with frequency larger than 65535 will be recorded as 65535. The program store all kmer frequency values in a 4^K size array of 16-bit integer (2 bytes), using the k-mer bit-value as index, so the total memory usage is 2* 4^K bytes. For K-mer size 15, 16, 17, 18, 19, it will consume constant 2G, 8G 32G 128G 512G memory, respectively. kmerfreq works in a highly simple and parallel style, to achieve as fast speed as possible. The output files can be used as input \file for programs GCE and correct_error_reads.
Environment Modules¶
Run module spider kmerfreq to find out what environment modules are available for this application.
System Variables¶
- HPC_KMERFREQ_DIR - installation directory
- HPC_KMERFREQ_BIN - executable directory