Workflows

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69 Workflows visible to you, out of a total of 79
Stable

Exome Alignment Workflow

Type: Common Workflow Language

Creator: Laura Rodriguez-Navas

Submitter: Laura Rodriguez-Navas

Stable

Summary

This notebook demonstrates how to retrieve metadata associated to the paper A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection and available in IDR at idr0094-ellinger-sarscov2. Over 300 compounds were used in this investigation. This notebook allows the user to calculate the half maximal inhibitory concentration (IC50) for ...

Type: Jupyter

Creators: Jean-Marie Burel, Andrea Zaliani

Submitter: Jean-Marie Burel

DOI: 10.48546/workflowhub.workflow.238.1

Stable

A hecatomb is a great sacrifice or an extensive loss. Heactomb the software empowers an analyst to make data driven decisions to 'sacrifice' false-positive viral reads from metagenomes to enrich for true-positive viral reads. This process frequently results in a great loss of suspected viral sequences / contigs.

For information about installation, usage, tutorial etc please refer to the documentation: https://hecatomb.readthedocs.io/en/latest/

Quick start guide

Install Hecatomb from Bioconda ...

Type: Snakemake

Creators: Michael Roach, Scott Handley, Rob Edwards

Submitter: Michael Roach

Work-in-progress

This workflow is dependent on other CWL workflows, see the git repository for these.

Workflow for Metagenomics from raw reads to annotated bins.

Main Steps

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (quality trimming)

  • bbmap contamination filter

  • SPAdes (Assembly)

  • QUAST (Assembly quality report)

  • BBmap (Read mapping to assembly)

  • MetaBat2 (binning)

  • CheckM (bin completeness and contamination)

  • GTDB-Tk (bin taxonomic classification)

Type: Common Workflow Language

Creators: Jasper Koehorst, Bart Nijsse

Submitter: Jasper Koehorst

This notebook is about pre-processing the Auditory Brainstem Response (ABR) raw data files provided by Ingham et. al to create a data set for Deep Learning models.

The unprocessed ABR data files are available at Dryad.

Since the ABR raw data are available as zip-archives, these have to be unzipped and the extracted raw data files parsed so that the time ...

Type: Jupyter

Creator: Elida Schneltzer

Submitter: Elida Schneltzer

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

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

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