Sibelia

NAME

DESCRIPTION

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> ...

(OR required)

Parameters set, used for the simplification. Option

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

(OR required)

File that contains manually chosen simplifications

parameters. See USAGE file for more information.

Directory where output files are written

Do not compute synteny blocks

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

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

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

Output sequences of synteny blocks (FASTA format).

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

Draw circos diagram with blocks at different stages.

Directory where temporary files are stored.

Value of K used for the synteny blocks inferring.

Output coordinates of synteny blocks from all stages

Use GFF format for reporting blocks coordinates

Do not perform postprocessing (stripe gluing).

Correct boundaries of unique synteny blocks.

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

Ignores the rest of the labeled arguments following this flag.

Displays version information and exits.

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