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Commit a2c01459 authored by Lihouck Flavien's avatar Lihouck Flavien
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Merge branch 'flihouck-main-patch-62949' into 'main'

Update README.md

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Dépot de travail pour versionner le travail réalisé pendant le stage Dépot de travail pour versionner le travail réalisé pendant le stage
## src ## Requirements
Version actuelle du pipeline meta-consensus This tool uses the Conda environment manager from the Anaconda software to run.
To install Conda check : https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
## Installation ## Installation
Voir comment réaliser un installeur facile a utiliser
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
Pour l'instant : dans un environnement avec snakemake installé: usage: mc_msa.py [-h] -input INPUT -output OUTPUT [-reference REFERENCE] [-size SIZE] [-list LIST]
Avec un dossier data situé dans le dossier parent contenant les données à utiliser. [-tools TOOLS] [-consensus_threshold CONSENSUS_THRESHOLD]
> snakemake --use-conda -c{nb coeurs} [-metaconsensus_threshold METACONSENSUS_THRESHOLD] [-depth DEPTH] [-plot PLOT]
[-region_overlap REGION_OVERLAP] [-cores CORES]
Creates the config file then runs the Meta-consensus pipeline
optional arguments:
-h, --help show this help message and exit
-input INPUT Reads file
-output OUTPUT Target directory for the pipeline results
-reference REFERENCE Reference for alignment and statistics
-list LIST A list of regions to work on (format: [r1, r2, ...] with r1 or [rStart1_End1, rStart2_End2 ...])
-size SIZE The size for cutting region (default: 2000)
(default: no region)
-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)
## Authors and acknowledgment ## Authors and acknowledgment
Show your appreciation to those who have contributed to the project. Flavien Lihouck
Special thanks to Coralie Rohmer's work on the tool MSA-limit, which inspired and was used in many parts of this project.
## License ## License
For open source projects, say how it is licensed. Probably CC_BY ?
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