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.