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Shotgun-Metagenomics-Analysis
Work-in-progress

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

DOI: 10.48546/workflowhub.workflow.327.1

BridgeDb tutorial: Gene HGNC name to Ensembl identifier
Work-in-progress

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 ...

Type: Jupyter

Creators: Marvin Martens, Egon Willighagen

Submitter: Marvin Martens

DOI: 10.48546/workflowhub.workflow.326.3

VGP HiFi phased assembly with hifiasm and HiC data

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP hybrid scaffolding with HiC data
Work-in-progress

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).

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP hybrid scaffolding with Bionano optical maps

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP purge assembly with purge_dups pipeline
Work-in-progress

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP HiFi phased assembly with hifiasm and HiC data
Work-in-progress

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

VGP genome profile analysis
Work-in-progress

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: Delphine Lariviere

Submitter: Cristóbal Gallardo

(old) SARS-COV2 version of the V-Pipe workflow

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

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eQTL-Catalogue/qtlmap

eQTL-Catalogue/qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

Introduction

eQTL-Catalogue/qtlmap is a bioinformatics analysis pipeline used for QTL Analysis.

The workflow takes phenotype count matrix (normalized and quality controlled) and genotype data as input, and finds associations between them with the help of sample metadata and phenotype metadata files (See Input formats and preparation for required input ...

Type: Nextflow

Creators: None

Submitter: Kaur Alasoo

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