| GMER_COUNTER(1) | GenomeTester User Manuals | GMER_COUNTER(1) |
gmer_counter - count k-mers from raw reads in FASTQ file
gmer_counter [OPTIONS] <SEQUENCES...>
-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
You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
glistquery(1), glistmaker(1), glistcompare(1), gmer_caller(1)
| 31 May 2018 | GenomeTester |