NAME

       gmer_counter - count k-mers from raw reads in FASTQ file

SYNOPSIS

       gmer_counter [OPTIONS] <SEQUENCES...>

OPTIONS

       -db DATABASE     - SNP/KMER database file

       -dbb DBBINARY    - binary database file

       -w FILENAME      - write binary database to file

       -32              - use 32-bit integeres for counts (default 16-bit)

       --max_kmers NUM  - maximum number of kmers per node

       --header         - print header row

       --total          - print the total number of kmers per node

       --unique         - print the number of nonzero kmers per node

       --kmers          - print individual kmer counts (default if no other output)

       --compile_index  - Add read index to database and write it to file

       --distribution NUM  - print kmer distribution (up to given number)

       --num_threads    - number of worker threads (default 24)

       --low_memory     - optimize for low memory usage

       -D               - increase debug level

EXAMPLES

        You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md

SEE ALSO

        glistquery(1), glistmaker(1), glistcompare(1), gmer_caller(1)

GenomeTester                                       31 May 2018                                   GMER_COUNTER(1)