Workflows
What is a Workflow?Filters
Type: Nextflow
Creators: Alem Gusinac, Thomas Ederveen, Jos Boekhorst, Annemarie Boleij
Submitter: Alem Gusinac
Evaluation of Pacbio Hifi Reads and genome profiling. Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses NCBI FCS GX to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.
This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format.
The bioinformatic workflow presented here enables the analysis of RNA sequencing data obtained from human reproductive tissues in unexplained recurrent pregnancy loss (uRPL) research. This pipeline requires a sample sheet containing the sample information (example_input_data.csv) and gene expression matrices generated using the Salmon tool in the nf-core/rnaseq bioinformatics pipeline (example_count_data.csv). For more information on how to use the nf-core/rnaseq pipeline including the required ...
Type: Nextflow
Creators: Jasmin Frangenberg, Anan Ibrahim, James A. Fellows Yates
Submitter: WorkflowHub Bot
WorkflowHub Knowledge Graph
A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.
Type: Snakemake
Creators: Alexander Hambley, Oliver Woolland, Eli Chadwick, Volodymyr Savchenko, José Mª Fernández, Stian Soiland-Reyes
Submitter: Eli Chadwick
Workflow for Metagenomics binning from assembly.
Minimal inputs are: Identifier, assembly (fasta) and an associated sorted BAM file
Summary
- MetaBAT2 (binning)
- MaxBin2 (binning)
- SemiBin2 (binning)
- Binette (bin merging)
- EukRep (eukaryotic classification)
- CheckM2 (bin completeness and contamination)
- BUSCO (bin completeness)
- GTDB-Tk (bin taxonomic classification)
- CoverM (bin abundances)
Including: Bin annotation (workflow: https://workflowhub.eu/workflows/1170):
- Bakta
...
Type: Common Workflow Language
Creators: Jasper Koehorst, Bart Nijsse
Submitters: Jasper Koehorst, Bart Nijsse
Type: Common Workflow Language
Creators: Ryo Mameda, Sora Yonezawa
Submitters: Sora Yonezawa, Ryo Mameda