Workflows
What is a Workflow?Filters
MRanalysis is an interactive R Shiny application designed for Mendelian randomization analysis.
MRanalysis
Mendelian randomization (MR) has emerged as a powerful epidemiological method for inferring causal relationships between exposures and outcomes using genome-wide association study (GWAS) summary data. By leveraging instrumental variables (IVs), such as single nucleotide polymorphisms (SNPs), MR can revolutionize our understanding of disease etiology, ...
This workflow analyses a given astrophysics text (e.g. Astronomer's Telegram https://astronomerstelegram.org/). It extracts positions of mentioned astronomical sources and provides possible optical counter-parts with photometric data. The corresponding photometric data can be further used to estimate the redshit of the optical sources, that is a measure of the distance between the Earth and the optical source.
Given the fact that the the tool that estimates the photometric redshift is still in ...
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 ...
Workflow for long read quality control, contamination filtering, assembly, variant calling and annotation.
Steps:
- Preprocessing of reference file : https://workflowhub.eu/workflows/1818
- LongReadSum before and after filtering (read quality control)
- Filtlong filter on quality and length
- Flye assembly
- Minimap2 mapping of reads and assembly
- Clair3 variant calling of reads
- Freebayes variant calling of assembly
- Optional Bakta annotation of genomes with no reference
- SnpEff building ...
**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.