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.