table of contents
| C-SIBELIA.PY(1) | User Commands | C-SIBELIA.PY(1) |
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:¶
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.
| February 2019 | C-Sibelia.py 3.0.7+ds |