Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
M
MC_MSA
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
GitLab community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Lihouck Flavien
MC_MSA
Commits
1500fc37
Commit
1500fc37
authored
3 years ago
by
Lihouck Flavien
Browse files
Options
Downloads
Patches
Plain Diff
Update README.md
parent
ee47cc40
No related branches found
No related tags found
No related merge requests found
Changes
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
README.md
+41
-45
41 additions, 45 deletions
README.md
with
41 additions
and
45 deletions
README.md
+
41
−
45
View file @
1500fc37
...
...
@@ -13,51 +13,47 @@ To install Conda check : https://docs.conda.io/projects/conda/en/latest/user-gui
You only need to download this repository in order to launch the pipeline, the first run will handle the setup for every tools using Conda.
## Usage
usage: mc_msa.py [-h] -input INPUT -output OUTPUT [-reference REFERENCE] [-size SIZE] [-list LIST]
[-tools TOOLS] [-consensus_threshold CONSENSUS_THRESHOLD]
[-metaconsensus_threshold METACONSENSUS_THRESHOLD] [-depth DEPTH] [-plot PLOT]
[-region_overlap REGION_OVERLAP] [-cores CORES]
usage: mc_msa -i INPUT -o OUTPUT [-r REFERENCE -t TOOLS ...]
Creates the config file then runs the Meta-consensus pipeline
optional arguments:
Required arguments:
-input INPUT, -i INPUT
> Reads file
-output OUTPUT, -o OUTPUT
> Target directory for the pipeline results
Standard arguments:
-h, --help
` show this help message and exit`
-input INPUT
` Reads file's path`
` (Required)`
-output OUTPUT
` Directory path for the pipeline results`
` (Required)`
-reference REFERENCE
` Reference file's path , for alignment and statistics `
> show this help message and exit
-reference REFERENCE, -r REFERENCE
> Reference for alignment and statistics
-tools TOOLS, -t TOOLS
> The list of tools to use in the meta-consensus
> (default: ['abpoa', 'spoa', 'kalign2', 'kalign3', 'mafft', 'muscle'])
-cores CORES, -c CORES
>The amount of cores to use in the pipeline run (default 1)
Advanced arguments:
-list LIST
` A list of regions to work on `
` (format: [r1, r2, ...] with r1 or [rStart1_End1, rStart2_End2 ...])`
` (default: no region)`
-size SIZE
` The size for cutting region`
` (default: 2000) `
-tools TOOLS
` The list of tools to use in the meta-consensus`
` (default: ['abpoa', 'spoa','kalign2', 'kalign3', 'mafft', 'muscle']) `
-consensus_threshold CONSENSUS_THRESHOLD
` Threshold(s) used for the MSA consensus step`
` (default: [70])`
-metaconsensus_threshold METACONSENSUS_THRESHOLD
` Threshold(s) used for the Meta-consensus result`
` (default: [60]) `
-depth DEPTH
` The depth used in the process`
` (default: [60]) `
-plot PLOT
` Analyse the meta-consensus and MSA consensus quality`
` (requires reference) `
-region_overlap REGION_OVERLAP
` The size of the overlap between regions `
-cores CORES
` The amount of cores to use in the pipeline run
`
(default 1)
`
> A list of regions to work on (format: [r1, r2, ...] or [rStart_End, ...]) (default: no region)
-size SIZE, -s SIZE
> The desired region size (default: maximum)
-consensus_threshold CONSENSUS_THRESHOLD, -ct CONSENSUS_THRESHOLD
> Threshold(s) used for the MSA consensus step (default: [70])
-metaconsensus_threshold METACONSENSUS_THRESHOLD, -mt METACONSENSUS_THRESHOLD
> Threshold(s) used for the Meta-consensus result (default: [60])
-depth DEPTH, -d DEPTH
> The depth used in the process (default: max)
### Input
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment