SEEK ID: https://workflowhub.eu/people/112
Location: Not specified
ORCID: Not specified
Joined: 12th Mar 2021
Expertise: Not specified
Tools: Not specified

Related items
Biodiversity Genomics Europe, funded by Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01, aims at aligning the resources and research agendas of both DNA barcoding and reference genome generation, thus opening the door for a true quantum leap in biodiversity genomics research in Europe.
Despite ground-breaking developments in both DNA barcoding and full genome sequencing, there remains a critical need to develop and strengthen functioning communities of practice ...
Teams: Vertebrate Genomes Pipelines in Galaxy, Biodiversity Genomics Europe (general)
Web page: https://biodiversitygenomics.eu/
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Teams: nf-core
Web page: https://nf-co.re
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Space: nf-core
Public web page: https://nf-co.re
Organisms: Not specified
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
Organisms: Not specified
The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database
Space: Biodiversity Genomics Europe (BGE)
Public web page: https://galaxyproject.org/projects/vgp/workflows/
Organisms: Not specified
Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.
Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).
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. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...
Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.
Type: Nextflow
Creators: Gisela Gabernet, Simon Heumos, Alexander Peltzer
Submitter: WorkflowHub Bot
This workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, ...
Type: Galaxy
Creators: Bérénice Batut, Paul Zierep, Mina Hojat Ansari, Patrick Bühler, Santino Faack
Submitter: WorkflowHub Bot
This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.
Workflow to predict EI mass spectra using QCxMS starting from a single SDF file, containing the 3D coordinates of all atoms in the molecule. These files can typically be obtained from PubChem.
Perform dcTMD free energy simulations and calculations
Type: Nextflow
Creators: Christopher Mohr, Alexander Peltzer, Sven Fillinger
Submitter: WorkflowHub Bot
Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...
Decontamination Workflow
Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.
Inputs
- Genome Assembly [fasta]
- Database for Kraken2. Database containing the possible contaminants.
Ouput
- List of contaminant scaffolds
- List of mitochondrial scaffolds
- Decontaminated assembly
Type: Nextflow
Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Bot
This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.