culebrONT
4.0.0
About CulebrONT
From assembly to correction
Assembly
Optional circularisation
Polishing
Correction
Quality Control of assemblies
Install
Requirements
Install CulebrONT PyPI package
Steps for installation
Steps for HPC distributed cluster installation
1. Adapt
profile
and
config.yaml
2. Adapt
tools_path.yaml
Check install
test_install
Advance installation
1. Snakemake profiles
Preparing the profile’s
config.yaml
file
2. Adapting
config.yaml
3. How to configure tools_path.yaml
And more …
How to build Apptainer images
Threading rules inside CulebrONT
Defining Workflows
How to create a workflow
create_config
1. Providing data
2. Choose assemblers, polisher and correctors
3. Choose quality control tools
4. Parameters for some specific tools
How to run the workflow
run
Advance run
Providing more resources
edit_profile
Providing your own tools_path.yaml
edit_tools
Output on CulebrONT
Report
Project Info
Citation
Useful notes
Thanks
License
FAQ
Frequently Asked Questions
API
culebrONT
create_config
edit_profile
edit_tools
install
run
show_tools
test_install
culebrONT
Index
Edit on GitLab
Index
Symbols
|
C
|
S
Symbols
--bash_completion
culebrONT-install command line option
--configfile
culebrONT-create_config command line option
,
[1]
culebrONT-run command line option
,
[1]
--data_dir
culebrONT-test_install command line option
,
[1]
--env
culebrONT-install command line option
--install_env
culebrONT command line option
--mode
culebrONT-install command line option
--no-bash_completion
culebrONT-install command line option
--pdf
culebrONT-run command line option
,
[1]
--restore
culebrONT command line option
culebrONT-edit_tools command line option
,
[1]
--version
culebrONT command line option
-c
culebrONT-create_config command line option
,
[1]
culebrONT-run command line option
,
[1]
-d
culebrONT-test_install command line option
,
[1]
-e
culebrONT command line option
culebrONT-install command line option
-m
culebrONT-install command line option
-pdf
culebrONT-run command line option
,
[1]
-r
culebrONT command line option
culebrONT-edit_tools command line option
,
[1]
-v
culebrONT command line option
C
culebrONT command line option
--install_env
--restore
--version
-e
-r
-v
culebrONT-create_config command line option
--configfile
,
[1]
-c
,
[1]
culebrONT-edit_tools command line option
--restore
,
[1]
-r
,
[1]
culebrONT-install command line option
--bash_completion
--env
--mode
--no-bash_completion
-e
-m
culebrONT-run command line option
--configfile
,
[1]
--pdf
,
[1]
-c
,
[1]
-pdf
,
[1]
SNAKEMAKE_OTHER
,
[1]
culebrONT-test_install command line option
--data_dir
,
[1]
-d
,
[1]
S
SNAKEMAKE_OTHER
culebrONT-run command line option
,
[1]