Sibelia1

Overview

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