Gene_fetch

This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).

Feature highlight

• Fetch protein and/or nucleotide sequences from NCBI GenBank database.
• Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...

Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 1 (WF7501) uses new data to create a multi-scale model of the Earth, which is used to update the REVEAL/CSEMv3 velocity model. The WF7501 workflow models an inversion-based update process for CSEMv3 (Computational Seismic Earth Model). Below is a simple explanation of the STEPs:

• ST750101 - Data Catalog Update: Collects external data sources and updates the database for further processing.
• ST750102 - Inversion Setup: Configures ...

Digitial Twin Component for Earthquakes (DTC-E) WorkFlow 2 (WF7502) generates synthetic shaking simulations (shakemaps) for seismic sources at different time scales, and automatically incorporates new data as it becomes available.

The workflow consists of multiple steps (ST), datasets (DT), and software services (SS). Below is a simplified breakdown:

Data Ingestion & Preprocessing

• ST750201: Assimilates real-time earthquake data from external sources.
• ST750202: Extracts earthquake ...

AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

• Protein evidence support
• RNASeq evidence support
• Statistics of the predictions (i.e., gene length, exon number, etc.)
• Ortholog analysis (BUSCO, OMArk)

Input data

• Reference genome genome.[.fna, .fa, .fasta]
• Annotation ...

sanger-tol/curationpretext

[![Cite with ...

[![Cite ...

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

• The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

CWL + RO-Crate Workflow Descriptions

This repository stores computational workflows described using the Common Workflow Language (CWL) and enriched with metadata using Research Object Crate (RO-Crate) conforming to the Workflow Run RO-Crate profile.

Each workflow is contained in its own directory (e.g., WF5201, WF6101, ...). Inside each workflow directory you will typically find at least:

• The CWL workflow definition (with the same name as the directory, e.g., WF5201.cwl). ...

Workflow to download and prepare TCGA data.

The workflow divides the process of generating Gene Regulatory networks from TCGA cancer data in three steps:

1. Downloading the raw data from GDC and saving the rds/tables needed later
2. Preparing the data. This step includes filtering the data, normalizing it...
3. Analysis of gene regulatory networks