NAME

       C-Sibelia.py - comparing two microbial genomes

DESCRIPTION

       usage: C-Sibelia.py [-h] [-s PARAMETERS] [-m MINBLOCKSIZE] [-p PROCESSCOUNT]

       [-i MAXITERATIONS] [--maf MAF] [-v VARIANT] [-u UNMAPPED]
              [--debug] [-t TEMPDIR | -o OUTDIR] reference assembly

       A tool for comparing two microbial genomes.

   positional arguments:
       reference
              A multi-FASTA file with the reference genome

       assembly
              A multi-FASTA file with the assembly genome

   optional arguments:
       -h, --help
              show this help message and exit

       -s PARAMETERS, --parameters PARAMETERS
              Parameters  set,  used  for the simplification. Option "loose" produces fewer blocks, but they are
              larger ("fine" is opposite). (default: fine)

       -m MINBLOCKSIZE, --minblocksize MINBLOCKSIZE
              Minimum size of a synteny block (default: 500)

       -p PROCESSCOUNT, --processcount PROCESSCOUNT
              Number of running processes (default: 1)

       -i MAXITERATIONS, --maxiterations MAXITERATIONS
              Maximum number of iterations during a stage of simplification (default: 4)

       --maf MAF
              Output file for storing alignments in MAF format (default: None)

       -v VARIANT, --variant VARIANT
              Output file with detected variants (default: variant.vcf)

       -u UNMAPPED, --unmapped UNMAPPED
              Output file for storing unmapped insertions in text format (default: None)

       --debug
              Generate output in text files (default: False)

       -t TEMPDIR, --tempdir TEMPDIR
              Directory for temporary files (default: None)

       -o OUTDIR, --outdir OUTDIR
              Directory for synteny block output files (default: None)

AUTHOR

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

C-Sibelia.py 3.0.7+ds                             February 2019                                  C-SIBELIA.PY(1)