Commit 07123ed3 authored by Rayan  CHIKHI's avatar Rayan CHIKHI

Update README.md

parent fafb4927
# Linked Reads molecule separation # Linked Reads molecule ordering
A compilation of scripts and pipelines to count and extract scaffolds of barcodes from linked reads datasets. A compilation of scripts and pipelines to extract orderings of barcodes from linked reads datasets.
**WARNING**: This code is a proof of concept, not a usable software for production. If the code is too slow for your tests or you are encontering some bugs (maybe it's a feature ? :p) don't hesitate to contact us via the issues or with a direct mail to me (yoann \[dot] dufresne \[at] pasteur \[dot] fr). **WARNING**: This code is a proof of concept, not a usable software for production. If the code is too slow
for your tests or you are encountering some bugs (maybe it's a feature ? :p)
don't hesitate to contact us via the issues or with a direct mail to me (yoann \[dot] dufresne \[at] pasteur \[dot] fr).
## Nomenclature warnings ## Nomenclature warnings
During the process of writing a scientific article, some of the datastructure names have been modified. During the process of writing the manuscript for this work, some of the data structures have been renamed.
In this repository the majority of the names are old names. In the code, old names might still be present.
So, here is a short list of equivalences: So, here is a short list of equivalences of terms:
- unit d-graph -> local clique pair - unit d-graph -> local clique pair
- udg -> lcp - udg -> lcp
- d²-graph (or d2-graph) -> lcp graph - d²-graph (or d2-graph) -> lcp graph
...@@ -50,9 +52,9 @@ Command to run the pipeline: ...@@ -50,9 +52,9 @@ Command to run the pipeline:
* generate_fake_barcode_graph.py: Take a barcode graph as input (gexf formatted) and outputs a barcode graph. The barcode graph is create by fusion of nodes from the molecule graph. * generate_fake_barcode_graph.py: Take a barcode graph as input (gexf formatted) and outputs a barcode graph. The barcode graph is create by fusion of nodes from the molecule graph.
* use the snakefile "Snakemake_data_simu". * use the snakefile "Snakemake_data_simu".
All the parameters can be an integer or a list of integer. All the parameters can be integers or lists of integers.
Each combination of parameter will generate a barcode graph. Each combination of parameters will generate a barcode graph.
Config parameters: The parameters are:
* n: the number of initial molecules * n: the number of initial molecules
* m: average number of node merged in each barcode * m: average number of node merged in each barcode
* d: average coverage of a molecule in the initial graph * d: average coverage of a molecule in the initial graph
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