How to count sequence read specific kmers from a single fasta file? I am working on Ulcerative Colitis Human Gut Microbiome data, where I have separate fasta files for separate patients. Each fasta contains a huge number of sequence reads with respective ids. I want to know the kmer counts for each sequence reads separately with their respective sequence IDs. Is there any software for that? Custom program takes too much time. Any help will be appreciated.