- 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.

Summary:

• 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

• SPAdes/Flye (Assembly)

• QUAST (Assembly quality report)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

• Metabat2/MaxBin2/SemiBin
• DAS Tool
• CheckM
• BUSCO
• 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:

Graphical abstract:

...

Snakemake workflow: Reconstructing raw tomography data

A Snakemake worfklow for tomographically reconstructing raw data using tomopy.

Installation

First download this repo and navigate to it

git clone https://codebase.helmholtz.cloud/gernha62/reconstructing-raw-tomography-data.git 

cd /path/to/repo 

(Optional) Download the example folder with:

wget -m -np https://doi2.psi.ch/datasets/das/work/p15/p15869/compression/MI04_02/tif
...

GermlineStructuralV-nf

:wrench: This pipeline is currently under development :wrench:

• Description
• Diagram
• User guide
• Infrastructure usage and recommendations
• Benchmarking
• Workflow summaries
• Metadata
• Component tools
• Additional notes
• Help/FAQ/Troubleshooting

...

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 ...

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

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.