Workflows

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1299 Workflows visible to you, out of a total of 1382

GERONIMO

Introduction

GERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.

The idea for developing GERONIMO emerged from a comprehensive search for [telomerase ...

Type: Snakemake

Creator: Agata Kilar

Submitter: Agata Kilar

DOI: 10.48546/workflowhub.workflow.547.1

Stable

Snakemake

About SnakeMAGs

SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available ...

Type: Snakemake

Creators: Nachida Tadrent, Franck Dedeine, Vincent Hervé

Submitter: Vincent Hervé

Stable

Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).


Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.552.1

Stable

Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).


Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

Type: Common Workflow Language

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.549.1

Stable

This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.

Stable

ARA (Automated Record Analysis) : An automatic pipeline for exploration of SRA datasets with sequences as a query

Requirements

or

  • Mamba package manager

  • Please checkout the mamba or micromamba official installation guide.

  • We prefer mamba over conda since it is faster and uses ...

Type: Perl

Creators: Anand Maurya, Maciej Szymanski, Wojciech Karlowski

Submitter: Anand Maurya

DOI: 10.48546/workflowhub.workflow.546.1

Stable

Simulations and figures supporting the manuscript "Timing of spring events changes under modelled future climate scenarios in a mesotrophic lake"

Type: Unrecognized workflow type

Creators: Jorrit Mesman, Inmaculada Jiménez-Navarro, Ana Ayala, Javier Senent-Aparicio, Dennis Trolle, Don Pierson

Submitter: Jorrit Mesman

DOI: 10.48546/workflowhub.workflow.511.5

Stable

Sample workflow template that combines simulations with data analytics. It is not a real workflow, but it mimics this type of workflows. It illustrates how COMPSs invokes binaries. It can be extended to invoke MPI applications.

Stable

BackTrackBB is a program for detection and space-time location of seismic sources based on multi-scale, frequency-selective statistical coherence of the wave field recorded by dense large-scale seismic networks and local antennas. The method is designed to enhance coherence of the signal statistical features across the array of sensors and consists of three steps. They are signal processing, space-time imaging and detection and location.

Source with inputs and outputs included (too big for ...

Work-in-progress

prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

  1. Download raw fastq files from SRA
  2. Trim and Filter raw fastq files using AdapterRemoval
  3. Align to the supplied genome using bowtie2
  4. Deduplicate Alignments using Picard MarkDuplicates
  5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...

Type: Snakemake

Creator: Stevie Pederson

Submitter: Stevie Pederson

DOI: 10.48546/workflowhub.workflow.528.1

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