---
name: "C-Sibelia.py"
section: "1"
platform: "linux"
package: "sibelia"
version: "3.0.7+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/C-Sibelia.py"
---

# C-Sibelia.py(1)

comparing two microbial genomes

## NAME

C-Sibelia.py - comparing two microbial genomes

## DESCRIPTION

usage: C-Sibelia.py \[-h\] \[-s PARAMETERS\] \[-m MINBLOCKSIZE\] \[-p PROCESSCOUNT\]

- \[-i MAXITERATIONS\] \[--maf MAF\] \[-v VARIANT\] \[-u UNMAPPED\]

  \[--debug\] \[-t TEMPDIR \| **-o** OUTDIR\] reference assembly

A tool for comparing two microbial genomes.

### positional arguments:

- reference

  A multi-FASTA file with the reference genome

- assembly

  A multi-FASTA file with the assembly genome

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-s** PARAMETERS, **--parameters** PARAMETERS

  Parameters set, used for the simplification. Option "loose" produces fewer blocks, but they are larger ("fine" is opposite). (default: fine)

- **-m** MINBLOCKSIZE, **--minblocksize** MINBLOCKSIZE

  Minimum size of a synteny block (default: 500)

- **-p** PROCESSCOUNT, **--processcount** PROCESSCOUNT

  Number of running processes (default: 1)

- **-i** MAXITERATIONS, **--maxiterations** MAXITERATIONS

  Maximum number of iterations during a stage of simplification (default: 4)

- **--maf** MAF

  Output file for storing alignments in MAF format (default: None)

- **-v** VARIANT, **--variant** VARIANT

  Output file with detected variants (default: variant.vcf)

- **-u** UNMAPPED, **--unmapped** UNMAPPED

  Output file for storing unmapped insertions in text format (default: None)

- **--debug**

  Generate output in text files (default: False)

- **-t** TEMPDIR, **--tempdir** TEMPDIR

  Directory for temporary files (default: None)

- **-o** OUTDIR, **--outdir** OUTDIR

  Directory for synteny block output files (default: None)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.