Workflows

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736 Workflows visible to you, out of a total of 791
Assemblosis

CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms

The workflow is designed to use both PacBio long-reads and Illumina short-reads. The workflow first extracts, corrects, trims and decontaminates the long reads. Decontaminated trimmed reads are then used to assemble the genome and raw reads are used to polish it. Next, Illumina reads are cleaned and used to further polish the resultant assembly. Finally, the polished assembly is masked using inferred repeats ...

Type: Common Workflow Language

Creator: Pasi Korhonen

Submitter: Pasi Korhonen

seurat scRNA-seq
Work-in-progress
No description specified

Type: Common Workflow Language

Creators: None

Submitter: panou@fleming.gr Panou

Python Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
Stable

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. ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.328.4

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

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