C-Sibelia.py1
Comparing two microbial genomes
Overview
usage: C-Sibelia.py [-h] [-s PARAMETERS] [-m MINBLOCKSIZE] [-p PROCESSCOUNT]
- [-i MAXITERATIONS] [--maf MAF] [-v VARIANT] [-u UNMAPPED]
-
[--debug] [-t TEMPDIR |
-oOUTDIR] 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)
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).