EnrichDO

EnrichDO is a double weighted iterative model by integrating the DO graph topology on a global scale. EnrichDO was based on the latest annotations of the human genome with DO terms, and double weighted the annotated genes. On one hand, to reinforce the saliency of direct gene-DO annotations, different initial weights were assigned to directly annotated genes and indirectly annotated genes, respectively. On the other hand, to detect locally most significant node between the ...

GALOP - Genome Assembly using Long reads Pipeline

This repository contains an exact copy of the standard Genoscope long reads assembly pipeline.

At the moment, this is not intended for users to download as it uses grid submission commands that will only work at Genoscope. As time goes on, we intend to make this pipeline available to a broader audience. However, genome assembly and polishing commands are accessible in the lib/assembly.py and lib/polishing.py files.

galop.py -h 
Mandatory
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cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...

This is an aggregation of the work done in Seq4AMR consisting of the following workflows:

• WF1: AbritAMR / AMRFinderPlus
• WF2: Sciensano (not currently included)
• WF3: SRST2
• WF4: StarAMR

Installation

• You will need to:
• run the [RGI Database ...

The Polygenic Score Catalog Calculator (pgsc_calc)

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Metagenome-Atlas

![Mastodon ...

Subset data on the Mediterreanean see and extract and visualise the Phosphate variable

Workflow permettant de prendre en entrée les résultats du challenge IA-biodiv par tâche, le fichier de référence par tâche afin de faire tourner un jupyter notebook produisant les scores pour chaque consortium participant.

beacon-omop-worker-survival-analysis

skim2mito

skim2mito is a snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes from low coverage genome skims. The pipeline was designed to work with sequence data from museum collections. However, it should also work with genome skims from recently collected samples.

Contents

• Setup
• Example data
• Input
• Output
• Filtering contaminants
• [Assembly and ...