Assembly — Editorial Board Home

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Editorial Board

orcid logoDelphine Lariviere avatar Delphine LariviereAnton Nekrutenko avatar Anton Nekrutenkoorcid logoTristan Reynolds avatar Tristan Reynolds

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Item Status Why you should do this
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Topic Materials

Material Contributions v2 Pre-requisites Follow up trainings Data on Zenodo Notebook Server Compatibility
An Introduction to Genome Assembly ✅ ✅
An introduction to get started in genome assembly and annotation ✅ ✅
Assembly of metagenomic sequencing data ✅ ✅
Assembly of the mitochondrial genome from PacBio HiFi reads ❌ ✅
Chloroplast genome assembly ✅ ✅
De Bruijn Graph Assembly ✅ ✅
Decontamination of a genome assembly ✅ ✅
Deeper look into Genome Assembly algorithms ❌ ✅
ERGA post-assembly QC ❌ ✅
Genome Assembly Quality Control ❌ ✅ ✅
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) ✅ ✅ ✅
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data ✅ ✅ ✅
Genome assembly and assembly QC - Introduction short version ✅ ✅
Genome assembly using PacBio data ✅ ✅ ❌
Hybrid genome assembly - Nanopore and Illumina ✅ ✅
Large genome assembly and polishing ✅ ✅
Making sense of a newly assembled genome ❌ ✅ ✅
Unicycler Assembly ✅ ✅ ✅
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads ❌ ✅ ✅
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data ❌ ✅
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step ✅ ✅

Topic Workflows

Material Workflow Updated Version Tests Reports Comments
An Introduction to Genome Assembly Intro to Genome Assembly Apr 3, 2026 5 ✅ ❌ ❌
Assembly of metagenomic sequencing data Assembly of metagenomic sequencing data Apr 3, 2026 0 ✅ ✅ ❌
Assembly of metagenomic sequencing data workflow-generate-dataset-for-assembly-tutorial Apr 3, 2026 0 ❌ ❌ ❌
Assembly of the mitochondrial genome from PacBio HiFi reads Mitogenome-Assembly-VGP0 Apr 3, 2026 1 ✅ ❌ ❌
Chloroplast genome assembly Chloroplast-genome-assembly-and-annotation Apr 3, 2026 3 ❌ ❌ ❌
De Bruijn Graph Assembly Debruijn Graph SPAdes Assembly Apr 3, 2026 1 ✅ ✅ ❌
De Bruijn Graph Assembly Debruijn Graph Velvet Full and SPAdes Assembly Apr 3, 2026 1 ✅ ✅ ❌
De Bruijn Graph Assembly Debruijn Graph Velvet Optimiser and SPAdes Assembly Apr 3, 2026 1 ✅ ✅ ❌
Decontamination of a genome assembly Assembly-decontamination-VGP9 Apr 3, 2026 1 ✅ ✅ ❌
ERGA post-assembly QC Post-assembly workflow Apr 3, 2026 2 ✅ ✅ ❌
Genome Assembly Quality Control Genome Assembly Quality Control Apr 3, 2026 1 ❌ ❌ ❌
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available) Apr 3, 2026 2 ✅ ✅ ❌
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Genome Assembly of MRSA using Illumina MiSeq Data Apr 3, 2026 3 ✅ ✅ ❌
Genome assembly using PacBio data Genome Assembly using PacBio data Apr 3, 2026 1 ✅ ❌ ❌
Hybrid genome assembly - Nanopore and Illumina Hybrid Genome Assembly Tutorial Workflow Apr 3, 2026 1 ✅ ✅ ✅
Large genome assembly and polishing Assembly polishing - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Assembly with Flye - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Assess genome quality - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Combined workflows for large genome assembly - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Data QC - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Racon polish with Illumina reads (R1 only), x2 - upgraded Apr 3, 2026 2 ❌ ❌ ❌
Large genome assembly and polishing Racon polish with long reads, x4 - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing Trim and filter reads - fastp - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Large genome assembly and polishing kmer counting - meryl - upgraded Apr 3, 2026 2 ❌ ✅ ❌
Making sense of a newly assembled genome Ecoli Comparison Apr 3, 2026 3 ❌ ❌ ❌
Unicycler Assembly Unicycler training Apr 3, 2026 4 ✅ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing Apr 3, 2026 1 ❌ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing_and_sra_download Apr 3, 2026 1 ❌ ❌ ❌
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step VGP assembly: training workflow Apr 3, 2026 4 ❌ ❌ ❌

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Learning Pathways using materials from this Topic

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Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

amr bacteria microgalaxy one-health microbiome
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Introduction to Galaxy and Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.

beginner introduction sequence-analysis assembly
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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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