Workflows

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134 Workflows visible to you, out of a total of 140

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Jasper Koehorst

DOI: 10.48546/workflowhub.workflow.154.2

Work-in-progress

This is an experimental KNIME workflow of using the BioExcel building blocks to implement the Protein MD Setup tutorial for molecular dynamics with GROMACS.

Note that this workflow won't import in KNIME without the experimental KNIME nodes for BioBB - contact Adam Hospital for details.

Stable

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers. Availability and Implementation: https://gitlab.com/vtilloy/aspicov

Type: Nextflow

Creators: Valentin Tilloy, Pierre Cuzin, Laura Leroi, Patrick Durand, Sophie Alain

Submitter: Valentin Tilloy

Stable

This PyCOMPSs workflow tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) in PyCOMPSs for execution on HPC. Three variants of the MD Setup workflows are included, supporting a list of structures, a list of mutations, or a cumulative set of mutations.

Stable

Analysis of RNA-seq data starting from BAM and focusing on mRNA, lncRNA and miRNA

Type: Galaxy

Creators: None

Submitter: Bianca Pasat

Stable

This BioExcel Building Blocks library (BioBB) workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium. The NAFlex pipeline was used for the preparation of all the simulations done in the study: ...

Stable

Summary

This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Drew Dickerson Dodecamer sequence -CGCGAATTCGCG- (PDB code 1BNA). The trajectory used is a 500ns-long MD simulation taken from the BigNASim database ...

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