Commit 34adf732 authored by Yoann Dufresne's avatar Yoann Dufresne

README update

parent 03f6d8de
......@@ -2,6 +2,8 @@
A compilation of scripts and pipelines to count and extract scaffolds 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).
## Nomenclature warnings
During the process of writing a scientific article, some of the datastructure names have been modified.
In this repository the majority of the names are old names.
......@@ -27,6 +29,20 @@ Install the package from the root directory.
For the majority of the scripts, argparse is used.
To know how to use it please use the -h command line option.
### Test the complete pipeline on simulated data
For a complete test, we made a bunch of snakemake files.
If you are looking for a complete pipeline from synthetic data generation, you should look into the "Snakefile_d2_eval" file.
You can play with the N (number of molecules in the interval graph), M (average number of merge to perform in a barcode), DEV (standard deviation on merge) variables to see impact on performances.
These values are arrays. You can enter multiple values and all the combinations will be done.
A summary is output in the tsv file "{WORKDIR}/eval_compare_maxclique.tsv.
Warning: the pipeline can be very slow for huge number of parameters.
Command to run the pipeline:
snakemake -s Snakefile_d2_eval
### Data simulation
* Create a linear molecule graph, where the molecules are linked to the d molecules on their left and d molecules on their right.
......@@ -3,8 +3,8 @@ include: "Snakefile_d2"
include: "Snakefile_d2_path"
WORKDIR = "snake_experiments" if "workdir" not in config else config["workdir"]
N = [500]
D = [6]
N = [5000]
D = [10]
M = [2]
DEV = [0]
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