.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH C-SIBELIA.PY "1" "February 2019" "C-Sibelia.py 3.0.7+ds" "User Commands"
.SH NAME
C-Sibelia.py \- comparing two microbial genomes
.SH DESCRIPTION
usage: C\-Sibelia.py [\-h] [\-s PARAMETERS] [\-m MINBLOCKSIZE] [\-p PROCESSCOUNT]
.TP
[\-i MAXITERATIONS] [\-\-maf MAF] [\-v VARIANT] [\-u UNMAPPED]
[\-\-debug] [\-t TEMPDIR | \fB\-o\fR OUTDIR]
reference assembly
.PP
A tool for comparing two microbial genomes.
.SS "positional arguments:"
.TP
reference
A multi\-FASTA file with the reference genome
.TP
assembly
A multi\-FASTA file with the assembly genome
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-s\fR PARAMETERS, \fB\-\-parameters\fR PARAMETERS
Parameters set, used for the simplification. Option
"loose" produces fewer blocks, but they are larger
("fine" is opposite). (default: fine)
.TP
\fB\-m\fR MINBLOCKSIZE, \fB\-\-minblocksize\fR MINBLOCKSIZE
Minimum size of a synteny block (default: 500)
.TP
\fB\-p\fR PROCESSCOUNT, \fB\-\-processcount\fR PROCESSCOUNT
Number of running processes (default: 1)
.TP
\fB\-i\fR MAXITERATIONS, \fB\-\-maxiterations\fR MAXITERATIONS
Maximum number of iterations during a stage of
simplification (default: 4)
.TP
\fB\-\-maf\fR MAF
Output file for storing alignments in MAF format
(default: None)
.TP
\fB\-v\fR VARIANT, \fB\-\-variant\fR VARIANT
Output file with detected variants (default:
variant.vcf)
.TP
\fB\-u\fR UNMAPPED, \fB\-\-unmapped\fR UNMAPPED
Output file for storing unmapped insertions in text
format (default: None)
.TP
\fB\-\-debug\fR
Generate output in text files (default: False)
.TP
\fB\-t\fR TEMPDIR, \fB\-\-tempdir\fR TEMPDIR
Directory for temporary files (default: None)
.TP
\fB\-o\fR OUTDIR, \fB\-\-outdir\fR OUTDIR
Directory for synteny block output files (default:
None)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.