.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH GMER_COUNTER "1" "31 May 2018" "GenomeTester" "GenomeTester User Manuals"
.SH NAME
gmer_counter \- count k-mers from raw reads in FASTQ file
.SH SYNOPSIS
.B gmer_counter
[\fI\,OPTIONS\/\fR] \fI\,<SEQUENCES...>\/\fR
.SH OPTIONS
.HP
\fB\-db\fR DATABASE     \- SNP/KMER database file
.HP
\fB\-dbb\fR DBBINARY    \- binary database file
.HP
\fB\-w\fR FILENAME      \- write binary database to file
.HP
\fB\-32\fR              \- use 32\-bit integeres for counts (default 16\-bit)
.HP
\fB\-\-max_kmers\fR NUM  \- maximum number of kmers per node
.HP
\fB\-\-header\fR         \- print header row
.HP
\fB\-\-total\fR          \- print the total number of kmers per node
.HP
\fB\-\-unique\fR         \- print the number of nonzero kmers per node
.HP
\fB\-\-kmers\fR          \- print individual kmer counts (default if no other output)
.HP
\fB\-\-compile_index\fR  \- Add read index to database and write it to file
.HP
\fB\-\-distribution\fR NUM  \- print kmer distribution (up to given number)
.HP
\fB\-\-num_threads\fR    \- number of worker threads (default 24)
.HP
\fB\-\-low_memory\fR     \- optimize for low memory usage
.HP
\fB\-D\fR               \- increase debug level
.SH EXAMPLES
 You could find some usage examples in /usr/share/doc/genometester/README.FastGT.md
.SH "SEE ALSO"
 \fBglistquery\fR(1), \fBglistmaker\fR(1), \fBglistcompare\fR(1), \fBgmer_caller\fR(1)