Sibelia - comparative genomics tool

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

Sibelia 3.0.7+ds                                  February 2019                                       SIBELIA(1)

       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

       Sibelia - comparative genomics tool