**Workflow for preprocessing a reference file. **

Steps: -When a GenBank file is not provided, it is downloaded from NCBI based on a accession number. -When multiple plasmid GenBank files are provided, they are merged into one file. -When any amount of plasmid GenBank files are provided, the reference is merged with the plasmid GenBank file(s) into one file. A FASTA file is also extracted. -When no plasmid Genbank files are provided, a FASTA file is extracted from the reference GenBank file. -A ...

PriorR

Priorr is a prioritization program of disease-linked genetic variants devoloped within the Genetics&Genomics Department of La Fundacion Jimenez Diaz University Hospital. Priorr is conceived to analyse the output of the FJD-pipeline of SNVs or CNVs. This software program offers a number of useful functionalities for variant analysis such as: filtering by a virtual panel of genes. manual control of different population frequencies or pathogenicity predictors or filtering out variants ...

GLOWgenes

Prioritization of gene diseases candidates by disease-aware evaluation of heterogeneous evidence networks Visit www.glowgenes.org for more information

Citing

de la Fuente L, Del Pozo-Valero M, Perea-Romero I, Blanco-Kelly F, Fernández-Caballero L, Cortón M, Ayuso C, Mínguez P. Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks. International Journal of Molecular Sciences. 2023; 24(2):1661. ...

WHALE: (W)orkflow for (H)uman-genome (A)nalysis of (L)ong-read (E)xperiments

Introduction

WHALE is a bioinformatics pipeline based on Nextflow and nf-core for long-read DNA sequencing analysis. It takes a samplesheet as input and performs quality control, alignment, variant calling and annotation.

Pipeline summary

1. Read QC (FastQC)
2. Present QC for raw reads (MultiQC)
3. Alignment ...

PARROT-FJD

Pipeline of Analysis and Research of Rare diseases Optimized in Tblab - Fundación Jiménez Díaz. This is a germline variant calling pipeline implemented in Nextflow which performs mapping, SNV/INDEL calling and annotation, and CNV calling and annotation for targeted sequencing (gene panels and WES) and whole genome sequencing.

How to run this pipeline

The different tasks previously mention are divided into different workflows which are specified usig the --analysis flag followed ...

Introduction

nf-CBRA-snvs (nf-core - CIBERER Bioinformatics for Rare diseases Analysis - Small Nucleotide Variant) is a workflow optimized for the analysis of rare diseases, designed to detect SNVs and INDELs in targeted sequencing data (CES/WES) as well as whole genome sequencing (WGS).

This pipeline is developed using Nextflow, a workflow management system that enables an easy execution across various computing environments. It uses Docker or Singularity containers, simplifying setup and ...

NanoFreeLunch

Detecting DNA modifications quantitatively from Nanopore data without using raw signals.

Installation

1. Install Julia from https://julialang.org/. Do Not use Julia in containers like docker or singularity.
2. Enter the folder of NanoFreeLunch and type julia setup.jl.
3. The executable can be found in build/bin/, add the folder to PATH or add softlink of the executable to the folder in your PATH.

Warning: you might experience slow package downloading or get error like ...

[!NOTE] All data files in the src/ethos/tokenize/maps directory are under the CC0 public domain waiver.

ETHOS - EHR foundation model

This repository implements Adaptive Risk Estimation System (ARES) for Hospital Mortality, ICU Admission, Prolonged Length of Stay, and Composite (HM+IU+PLoS). In addition, it contains all the experiments conducted in our paper (preprint). It builds on our previous work on EHR foundation models by completely reimplementing ...

FREEPII (Feature Representation Enhancement End-to-end Protein Interaction Inference) is an end-to-end learning method encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference.

Portable genotype-free demultiplexing benchmarkign pipeline.

A portable pipeline for benchmarking genotype-free single-cell demultiplexing methods on simulated data.

The pipeline is designed to be generelisable to different datasets with arbitrary numbers of simulated mulitplexed samples. All software as part of pipeline is run through Apptainer containers to ensure reproducibility and ease of use. The pipeline default configuration is to be run on a cluster with a SLURM scheduler, but can be ...