.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH TWOPACO "1" "September 2022" "twopaco 1.0.0" "User Commands"
.SH NAME
twopaco \- build the compacted de Bruijn graph from many complete genomes
.SH DESCRIPTION
USAGE:
.TP
twopaco
{\-f <integer>|\-\-filtermemory <float>} [\-o <file name>] [\-\-test]
[\-\-tmpdir <directory name>] [\-a <integer>] [\-t <integer>] [\-r
<integer>] [\-q <integer>] [\-k <oddc>] [\-\-] [\-\-version] [\-h]
<fasta files with genomes> ...
.PP
Where:
.HP
\fB\-f\fR <integer>,  \fB\-\-filtersize\fR <integer>
.TP
(OR required)
Size of the filter
.HP
\fB\-\-\fR OR \fB\-\-\fR
.HP
\fB\-\-filtermemory\fR <float>
.TP
(OR required)
Memory in GBs allocated for the filter
.HP
\fB\-o\fR <file name>,  \fB\-\-outfile\fR <file name>
.IP
Output file name prefix
.HP
\fB\-\-test\fR
.IP
Run tests
.HP
\fB\-\-tmpdir\fR <directory name>
.IP
Temporary directory name
.HP
\fB\-a\fR <integer>,  \fB\-\-abundance\fR <integer>
.IP
Vertex abundance threshold
.HP
\fB\-t\fR <integer>,  \fB\-\-threads\fR <integer>
.IP
Number of worker threads
.HP
\fB\-r\fR <integer>,  \fB\-\-rounds\fR <integer>
.IP
Number of computation rounds
.HP
\fB\-q\fR <integer>,  \fB\-\-hashfnumber\fR <integer>
.IP
Number of hash functions
.HP
\fB\-k\fR <oddc>,  \fB\-\-kvalue\fR <oddc>
.IP
Value of k
.HP
\fB\-\-\fR,  \fB\-\-ignore_rest\fR
.IP
Ignores the rest of the labeled arguments following this flag.
.HP
\fB\-\-version\fR
.IP
Displays version information and exits.
.HP
\fB\-h\fR,  \fB\-\-help\fR
.IP
Displays usage information and exits.
.TP
<fasta files with genomes>
(accepted multiple times)
.TP
(required)
FASTA file(s) with nucleotide sequences.
.IP
Program for construction of the condensed de Bruijn graph from complete
genomes
.SH AUTHOR
 This manpage was written by Andrius Merkys for the Debian distribution and
 can be used for any other usage of the program.