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
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
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
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
Organisms: Not specified
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
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.
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.
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).
Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). The contigs are purged from the first assembly (hap1, pri...), added to the second assembly (hp2, alt... ), then the 2nd assembly is purged as well. If you think only one of the assemblies needs purging, use the VGP6b workflow. 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 quality and contamination control analysis on assembled contigs to assess bacterial genome quality and taxonomic assignment
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation directly from raw reads
Type: Galaxy
Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium
Submitter: WorkflowHub Bot
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
Complete ChIP-seq analysis for single-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and quality filtering (MAPQ >= 30). Peak calling with MACS2 uses either a fixed extension parameter or built-in model to identify protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.
Complete ChIP-seq analysis for paired-end sequencing data. Processes raw FASTQ files through adapter removal (cutadapt), alignment to reference genome (Bowtie2), and stringent quality filtering (MAPQ >= 30, concordant pairs only). Peak calling with MACS2 optimized for paired-end reads identifies protein-DNA binding sites. Generates alignment files, peak calls, and quality metrics for downstream analysis.
Find and annotate variants in ampliconic SARS-CoV-2 Illumina sequencing data and classify samples with pangolin and nextclade
Variant calling and consensus sequence generation for batches of Illumina PE sequenced viruses with uncomplicated and stable genome structure (like e.g. Morbilliviruses).
COVID-19: variation analysis on ARTIC ONT data
This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...
This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.
This workflow performs subtyping and consensus sequence generation for batches of Illumina PE sequenced Influenza A isolates.
Type: Galaxy
Creators: Viktoria Isabel Schwarz, Wolfgang Maier, Aaron Kolbecher, Saim Momin
Submitter: WorkflowHub Bot
A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach
This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq
Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.
This workflow takes a VCF dataset of variants produced by any of the *-variant-calling workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular lists of variants by Samples and by Variant, and an overview plot of variants and their allele-frequencies.
RepeatMasking Workflow
This workflow uses RepeatModeler and RepeatMasker for genome analysis.
-
RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.
-
RepeatMasker is a program that analyzes ...