Workflows

Genome Assembly of MRSA using Illumina MiSeq Data

Associated Tutorial

This workflows is part of the tutorial Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data, available in the GTN

Features

• Includes Galaxy Workflow Tests

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Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Associated Tutorial

This workflows is part of the tutorial Quality and contamination control in bacterial isolate using Illumina MiSeq Data, available in the GTN

Features

• Includes [Galaxy Workflow ...

Mapping

Associated Tutorial

This workflows is part of the tutorial Mapping, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

Associated Tutorial

This workflows is part of the tutorial Formation of the Super-Structures on the Inactive X, available in the GTN

Features

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

atac-seq

Associated Tutorial

This workflows is part of the tutorial ATAC-Seq data analysis, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

Associated Tutorial

This workflows is part of the tutorial Remove contamination and host reads, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a Galaxy Workflow Report ...

This workflow performs taxonomic profiling of metagenomic data and visualizes microbial community composition using Kraken2 and Bracken as well as MetaPhlAn.

Associated Tutorial

This workflows is part of the tutorial Taxonomic Profiling and Visualization of Metagenomic Data, available in the GTN

Features

• Includes [Galaxy Workflow ...

Checking expected species and contamination in bacterial isolate

Associated Tutorial

This workflows is part of the tutorial Checking expected species and contamination in bacterial isolate, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Identification of AMR genes in an assembled bacterial genome

Associated Tutorial

This workflows is part of the tutorial Identification of AMR genes in an assembled bacterial genome, available in the GTN

Features

• Includes Galaxy Workflow Tests ...

Workflow for processing amplicon pool sequencing data without reference sequence.

This workflow allows you to reconstruct a sequence from an amplicon pool without a reference sequence. To run this workflow, you need the reads from the pool library you want to analyse in FASTQ format, separated into two files: forward and reverse. You will also need the primers used during sequencing. This workflow creates one or two contigs (depending on whether your primers were used once or twice) and a metadata ...