WorkflowsWhat is a Workflow?
- Deprecated -
See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367
And other workflows: https://workflowhub.eu/projects/16#workflows
Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning
- Workflow Nanopore Quality
- Kraken2 taxonomic classification of FASTQ reads
- Flye (de-novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Workflow ...
Workflow for Illumina Quality Control and Filtering
Multiple paired datasets will be merged into single paired dataset.
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
Workflow for LongRead Quality Control and Filtering
- FastQC before filtering (read quality control)
- Filtlong (read trimming)
- Kraken2 taxonomic read classification
- Minimap2 read filtering based on given references
- FastQC after filtering (read quality control)
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: ...
Workflow (hybrid) metagenomic assembly and binning + GEMs
Accepts both Illumina and Nanopore
Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
Workflow LongRead Quality: https://workflowhub.eu/workflows/337
Kraken2 taxonomic classification of FASTQ reads
QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- DAS Tool
- GTDB-Tk ...
1. About TF-Prioritizer
This pipeline gives you a full analysis of nfcore chromatine accessibility peak data (ChIP-Seq, ATAC-Seq or DNAse-Seq) and nfcore RNA-seq count data. It performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform the data. It also gives you plots for deep analysis of the data. The general workflow is sketched in the images below:
Type: Unrecognized workflow type
Submitter: Nico Trummer
Snakemake workflow: Reconstructing raw tomography data
A Snakemake worfklow for tomographically reconstructing raw data using tomopy.
First download this repo and navigate to it
git clone https://codebase.helmholtz.cloud/gernha62/reconstructing-raw-tomography-data.git
(Optional) Download the example folder with:
wget -m -np https://doi2.psi.ch/datasets/das/work/p15/p15869/compression/MI04_02/tif ...
:wrench: This pipeline is currently under development :wrench:
- User guide
- Infrastructure usage and recommendations
- Workflow summaries
- Component tools
- Additional notes
We present an R script that describes the workflow for analysing honey bee (Apis mellifera) wing shape. It is based on a large dataset of wing images and landmark coordinates available at Zenodo: https://doi.org/10.5281/zenodo.7244070. The dataset can be used as a reference for the identification of unknown samples. As unknown samples, we used data from Nawrocka et al. (2018), available at Zenodo: https://doi.org/10.5281/zenodo.7567336. Among others, the script can be used to identify the geographic ...
Type: R markdown
Submitter: Adam Tofilski
This workflow take as input a collection of paired fastq. It uses HiCUP to go from fastq to validPair file. The pairs are filtered for MAPQ and sorted by cooler to generate a tabix dataset. Cooler is used to generate a balanced cool file to the desired resolution.