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/
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
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
Organisms: Not specified
Scaffolding using HiC data with YAHS.
Contiging Solo w/HiC:
Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.
Inputs
- Hifi long reads [fastq]
- HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
- HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Name of first assembly
- Name of second ...
Scaffolding with Bionano
Scaffolding using Bionano optical map data
Inputs
- Bionano data [cmap]
- Estimated genome size [txt]
- Phased assembly generated by Hifiasm [gfa1]
Outputs
- Scaffolds
- Non-scaffolded contigs
- QC: Assembly statistics
- QC: Nx plot
- QC: Size plot
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). 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)
Purge Duplicate Contigs
Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) 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)
Inputs
- Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
- Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
- Assembly to purge (e.g. hap1) ...
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...
Assembly with Hifi reads and Trio Data
Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing
Inputs
- Hifi long reads [fastq]
- Concatenated Illumina reads : Paternal [fastq]
- Concatenated Illumina reads : Maternal [fastq]
- K-mer database [meryldb]
- Paternal hapmer database [meryldb]
- Maternal hapmer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Bloom Filter
- Name of first haplotype
- Name of second haplotype ...
dada2 amplicon analysis for paired end data
The workflow has three main outputs:
- the sequence table (output of makeSequenceTable)
- the taxonomy (output of assignTaxonomy)
- the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)
This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html
Assemble long reads with Flye, then view assembly statistics and assembly graph
Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.
This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.
Type: Galaxy
Creators: Lucille Delisle, Mehmet Tekman, Hans-Rudolf Hotz, Daniel Blankenberg, Wendi Bacon
Submitter: WorkflowHub Bot
This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.
MMGBSA simulation and calculation
VGP Workflow #1
This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
Inputs
- A collection of Hifi long reads in FASTQ format
- k-mer length
- Ploidy
Outputs
- Meryl Database of kmer counts
...
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).
Contiging Solo w/HiC:
Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.
Inputs
- Hifi long reads [fastq]
- HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
- HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
- K-mer database [meryldb]
- Genome profile summary generated by Genomescope [txt]
- Name of first assembly
- Name of second assembly ...