.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SIBELIA "1" "February 2019" "Sibelia 3.0.7+ds" "User Commands"
.SH NAME
Sibelia \- comparative genomics tool
.SH DESCRIPTION
USAGE:
.TP
Sibelia
{\-s <loose|fine|far>|\-k <file name>} [\-o <dir name>]
[\-\-noblocks] [\-r] [\-a] [\-m <integer>] [\-q] [\-g] [\-v] [\-t <dir
name>] [\-\-lastk <integer > 1>] [\-\-allstages] [\-\-gff]
[\-\-nopostprocess] [\-\-correctboundaries] [\-i <integer > 0>] [\-\-]
[\-\-version] [\-h] <fasta files with genomes> ...
.PP
Where:
.HP
\fB\-s\fR <loose|fine|far>,  \fB\-\-parameters\fR <loose|fine|far>
.TP
(OR required)
Parameters set, used for the simplification. Option
.IP
"loose" produces fewer blocks, but they are larger ("fine" is
opposite).
.HP
\fB\-\-\fR OR \fB\-\-\fR
.HP
\fB\-k\fR <file name>,  \fB\-\-stagefile\fR <file name>
.TP
(OR required)
File that contains manually chosen simplifications
.IP
parameters. See USAGE file for more information.
.HP
\fB\-o\fR <dir name>,  \fB\-\-outdir\fR <dir name>
.IP
Directory where output files are written
.HP
\fB\-\-noblocks\fR
.IP
Do not compute synteny blocks
.HP
\fB\-r\fR,  \fB\-\-inram\fR
.IP
Perform all computations in RAM, don't create temp files.
.HP
\fB\-a\fR,  \fB\-\-sharedonly\fR
.IP
Output only blocks that occur exactly once in each input sequence.
.HP
\fB\-m\fR <integer>,  \fB\-\-minblocksize\fR <integer>
.IP
Minimum size of a synteny block, default value = 5000 BP.
.HP
\fB\-q\fR,  \fB\-\-sequencesfile\fR
.IP
Output sequences of synteny blocks (FASTA format).
.HP
\fB\-g\fR,  \fB\-\-graphfile\fR
.IP
Output resulting condensed de Bruijn graph (in dot format).
.HP
\fB\-v\fR,  \fB\-\-visualize\fR
.IP
Draw circos diagram with blocks at different stages.
.HP
\fB\-t\fR <dir name>,  \fB\-\-tempdir\fR <dir name>
.IP
Directory where temporary files are stored.
.HP
\fB\-\-lastk\fR <integer > 1>
.IP
Value of K used for the synteny blocks inferring.
.HP
\fB\-\-allstages\fR
.IP
Output coordinates of synteny blocks from all stages
.HP
\fB\-\-gff\fR
.IP
Use GFF format for reporting blocks coordinates
.HP
\fB\-\-nopostprocess\fR
.IP
Do not perform postprocessing (stripe gluing).
.HP
\fB\-\-correctboundaries\fR
.IP
Correct boundaries of unique synteny blocks.
.HP
\fB\-i\fR <integer > 0>,  \fB\-\-maxiterations\fR <integer > 0>
.IP
Maximum number of iterations during a stage of simplification, default
= 4.
.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 finding syteny blocks in closely related genomes
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.