npm

jellyfish

Fast, memory-efficient counting of DNA k-mers in sequencing data

brewmacoslinux
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Fast, memory-efficient counting of DNA k-mers

Commands

jellyfish

Examples

Count 21-mers in a FASTA file and output results$ jellyfish count -m 21 -s 100M -t 4 -o kmers.jf sequence.fasta
Dump k-mer counts to a text file in fasta format$ jellyfish dump -c kmers.jf > kmers.fasta
Query the frequency of a specific k-mer$ jellyfish query -o output.txt kmers.jf ACGTACGTACGTACGTACGT