Workflows

What is a Workflow?
1294 Workflows visible to you, out of a total of 1377

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, ...

Type: Docker

Creator: Abao Xing

Submitter: Abao Xing

DOI: 10.48546/workflowhub.workflow.1872.1

Stable

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 ...

Type: Galaxy

Creator: Andrei Variu

Submitter: Andrei Variu

DOI: 10.48546/workflowhub.workflow.1353.2

Imputation Workflow h3abionet/chipimputation

Nextflow Docker fair-software.eu

Introduction

Imputation is likely to be run ...

Type: Nextflow

Creators: None

Submitter: Takudzwa Musarurwa

GitHub Actions CI Status GitHub Actions Linting StatusAWS CI[![Cite ...

Type: Nextflow

Creator: Phil Ewels

Submitter: WorkflowHub Bot

Stable

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 ...

Type: Docker

Creators: None

Submitter: Yolanda Benítez Quesada

Work-in-progress

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 ...

Type: Common Workflow Language

Creator: Martijn Melissen

Submitter: Martijn Melissen

**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 ...

Type: Common Workflow Language

Creator: Martijn Melissen

Submitter: Martijn Melissen

Stable

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 ...

Type: Docker

Creators: None

Submitter: Yolanda Benítez Quesada

Stable

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. ...

Type: Python

Creators: None

Submitter: Yolanda Benítez Quesada

Work-in-progress

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 ...

Type: Nextflow

Creators: None

Submitter: Yolanda Benítez Quesada

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