gmer_counter1
Count k-mers from raw reads in fastq file
Usage
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
Releases
Unchanged in 4 releases since Debian 10 (Buster).