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

# Sibelia(1)

comparative genomics tool

## NAME

Sibelia - comparative genomics tool

## DESCRIPTION

USAGE:

- 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\> ...

Where:

**-s** \<loose\|fine\|far\>,  **--parameters** \<loose\|fine\|far\>

- (OR required)

  Parameters set, used for the simplification. Option

-

  "loose" produces fewer blocks, but they are larger ("fine" is opposite).

**--** OR **--**

**-k** \<file name\>,  **--stagefile** \<file name\>

- (OR required)

  File that contains manually chosen simplifications

-

  parameters. See USAGE file for more information.

**-o** \<dir name\>,  **--outdir** \<dir name\>

-

  Directory where output files are written

**--noblocks**

-

  Do not compute synteny blocks

**-r**,  **--inram**

-

  Perform all computations in RAM, don't create temp files.

**-a**,  **--sharedonly**

-

  Output only blocks that occur exactly once in each input sequence.

**-m** \<integer\>,  **--minblocksize** \<integer\>

-

  Minimum size of a synteny block, default value = 5000 BP.

**-q**,  **--sequencesfile**

-

  Output sequences of synteny blocks (FASTA format).

**-g**,  **--graphfile**

-

  Output resulting condensed de Bruijn graph (in dot format).

**-v**,  **--visualize**

-

  Draw circos diagram with blocks at different stages.

**-t** \<dir name\>,  **--tempdir** \<dir name\>

-

  Directory where temporary files are stored.

**--lastk** \<integer \> 1\>

-

  Value of K used for the synteny blocks inferring.

**--allstages**

-

  Output coordinates of synteny blocks from all stages

**--gff**

-

  Use GFF format for reporting blocks coordinates

**--nopostprocess**

-

  Do not perform postprocessing (stripe gluing).

**--correctboundaries**

-

  Correct boundaries of unique synteny blocks.

**-i** \<integer \> 0\>,  **--maxiterations** \<integer \> 0\>

-

  Maximum number of iterations during a stage of simplification, default = 4.

**--**,  **--ignore\_rest**

-

  Ignores the rest of the labeled arguments following this flag.

**--version**

-

  Displays version information and exits.

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

-

  Displays usage information and exits.

- \<fasta files with genomes\>

  (accepted multiple times)

- (required)

  FASTA file(s) with nucleotide sequences.

-

  Program for finding syteny blocks in closely related genomes

## AUTHOR

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