Workflows
What is a Workflow?Filters
VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing
VIsoQLR is an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies ...
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
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
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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 ...
