Workflows
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Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
Based on the official pmx tutorial.
This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial. ...
Shotgun Metagenomics Analysis
Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
Description
The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!
These scripts have been written ...
Type: Shell Script
Creators: Cali Willet, Rosemarie Sadsad, Tracy Chew, Smitha Sukumar, Elena Martinez, Christina Adler, Henry Lydecker, Fang Wang
Submitter: Tracy Chew
BridgeDb tutorial: Gene HGNC name to Ensembl identifier
This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers. This step is part of the OpenRiskNet use case to link Adverse Outcome Pathways to WikiPathways.
First we need to load the Python library to allow calls to the BridgeDb REST webservice:
import requests
Let's assume we're interested ...
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).
Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.
Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
A version of V-pipe (analysis of next generation sequencing (NGS) data from viral pathogens) specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2.
Type: Snakemake
Creators: Ivan Topolsky, Susana Posada Céspedes, Niko Beerenwinkel,
Submitter: Hervé Ménager