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 ✅ ✅ ❌
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 Aug 2, 2025 5 ✅ ❌ ❌
Assembly of metagenomic sequencing data Assembly of metagenomic sequencing data Aug 2, 2025 0 ✅ ✅ ❌
Assembly of metagenomic sequencing data workflow-generate-dataset-for-assembly-tutorial Aug 2, 2025 0 ❌ ❌ ❌
Assembly of the mitochondrial genome from PacBio HiFi reads Mitogenome-Assembly-VGP0 Aug 2, 2025 1 ✅ ❌ ❌
Chloroplast genome assembly Chloroplast-genome-assembly-and-annotation Aug 2, 2025 3 ❌ ❌ ❌
De Bruijn Graph Assembly Debruijn Graph Aug 2, 2025 4 ✅ ❌ ❌
Decontamination of a genome assembly Assembly-decontamination-VGP9 Aug 2, 2025 1 ✅ ✅ ❌
ERGA post-assembly QC Post-assembly workflow Aug 2, 2025 2 ✅ ✅ ❌
Genome Assembly Quality Control Genome Assembly Quality Control Aug 2, 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) Aug 2, 2025 1 ✅ ❌ ❌
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Genome Assembly of MRSA using Illumina MiSeq Data Aug 2, 2025 2 ✅ ❌ ❌
Genome assembly using PacBio data Genome Assembly using PacBio data Aug 2, 2025 1 ✅ ❌ ❌
Large genome assembly and polishing Assembly polishing - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assembly with Flye - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assess genome quality - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Combined workflows for large genome assembly - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Data QC - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Racon polish with Illumina reads (R1 only), x2 - upgraded Aug 2, 2025 2 ❌ ❌ ❌
Large genome assembly and polishing Racon polish with long reads, x4 - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Trim and filter reads - fastp - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing kmer counting - meryl - upgraded Aug 2, 2025 2 ❌ ✅ ❌
Making sense of a newly assembled genome Ecoli Comparison Aug 2, 2025 3 ❌ ❌ ❌
Unicycler Assembly Unicycler training Aug 2, 2025 4 ✅ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing Aug 2, 2025 1 ❌ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing_and_sra_download Aug 2, 2025 1 ❌ ❌ ❌
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step VGP assembly: training workflow Aug 2, 2025 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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