Workflows

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Workflow for the Galaxy Training Network tutorial "Hybrid genome assembly - Nanopore and Illumina"

Associated Tutorial

This workflows is part of the tutorial Hybrid genome assembly - Nanopore and Illumina, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Visualize and filter scATAC-seq anndata to produce a high quality count matrix

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

This workflow creates an count matrix anndata file given 10x scATAC-seq data.

Associated Tutorial

This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

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.

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.

To perform Qualification, Nitrate Calibration, Validation of One Argo float or One Glider by using Neural Network and Climatology. Copy past before running and change calibration parametrization if necessary

Associated Tutorial

This workflows is part of the tutorial Nitrate DMQC for autonomous platforms such as Argo floats, available in the GTN ...

Generate mitochondrial assembly based on PacBio HiFi reads. Part of the VGP suite, it can be run at any time independently of the other workflows. This workflow uses MitoHiFi and a mitochondrial reference to assemble the mitochondrial genome from PacBio reads. You do not need to provide the reference yourself, only the Latin name of the species.

This workflow performs quality and contamination control analysis on assembled contigs to assess bacterial genome quality and taxonomic assignment

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation directly from raw reads