Assembly — Editorial Board Home

This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.

Editorial Board

orcid logoDelphine Lariviere avatar Delphine LariviereAnton Nekrutenko avatar Anton Nekrutenko

Action Items

Item Status Why you should do this
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Sufficient Editorial Board Members More required ❌ Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
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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 Nov 21, 2025 5 ✅ ❌ ❌
Assembly of metagenomic sequencing data Assembly of metagenomic sequencing data Nov 21, 2025 0 ✅ ✅ ❌
Assembly of metagenomic sequencing data workflow-generate-dataset-for-assembly-tutorial Nov 21, 2025 0 ❌ ❌ ❌
Assembly of the mitochondrial genome from PacBio HiFi reads Mitogenome-Assembly-VGP0 Nov 21, 2025 1 ✅ ❌ ❌
Chloroplast genome assembly Chloroplast-genome-assembly-and-annotation Nov 21, 2025 3 ❌ ❌ ❌
De Bruijn Graph Assembly Debruijn Graph Nov 21, 2025 4 ✅ ❌ ❌
Decontamination of a genome assembly Assembly-decontamination-VGP9 Nov 21, 2025 1 ✅ ✅ ❌
ERGA post-assembly QC Post-assembly workflow Nov 21, 2025 2 ✅ ✅ ❌
Genome Assembly Quality Control Genome Assembly Quality Control Nov 21, 2025 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) Nov 21, 2025 1 ✅ ❌ ❌
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Genome Assembly of MRSA using Illumina MiSeq Data Nov 21, 2025 2 ✅ ❌ ❌
Genome assembly using PacBio data Genome Assembly using PacBio data Nov 21, 2025 1 ✅ ❌ ❌
Hybrid genome assembly - Nanopore and Illumina Hybrid Genome Assembly Tutorial Workflow Nov 21, 2025 1 ✅ ✅ ✅
Large genome assembly and polishing Assembly polishing - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assembly with Flye - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assess genome quality - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Combined workflows for large genome assembly - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Data QC - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Racon polish with Illumina reads (R1 only), x2 - upgraded Nov 21, 2025 2 ❌ ❌ ❌
Large genome assembly and polishing Racon polish with long reads, x4 - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Trim and filter reads - fastp - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing kmer counting - meryl - upgraded Nov 21, 2025 2 ❌ ✅ ❌
Making sense of a newly assembled genome Ecoli Comparison Nov 21, 2025 3 ❌ ❌ ❌
Unicycler Assembly Unicycler training Nov 21, 2025 4 ✅ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing Nov 21, 2025 1 ❌ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing_and_sra_download Nov 21, 2025 1 ❌ ❌ ❌
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step VGP assembly: training workflow Nov 21, 2025 4 ❌ ❌ ❌

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Learning Pathways using materials from this Topic

GTN logo with a multi-coloured star and the words Galaxy Training Network
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
GTN logo with a multi-coloured star and the words Galaxy Training Network
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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