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 logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton Nekrutenko

Action Items

Item Status Why you should do this
Summary Done ✅ Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic.
Sufficient Editorial Board Members Done ✅ (4 members) Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term.
Enable Subtopics Pending ❌ Subtopics help organize the content and make it easier to navigate.
Annotate Funders Done ✅ (3 funders) By annotating the funders of your topic's materials, you make it easier to write your grant reports later
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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 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 Jan 22, 2025 5 ✅ ❌ ❌
Assembly of metagenomic sequencing data Metagenomics assembly tutorial workflow Jan 22, 2025 0 ❌ ❌ ❌
Assembly of metagenomic sequencing data workflow-generate-dataset-for-assembly-tutorial Jan 22, 2025 0 ❌ ❌ ❌
Assembly of the mitochondrial genome from PacBio HiFi reads Mitogenome-Assembly-VGP0 Jan 22, 2025 1 ✅ ❌ ❌
Chloroplast genome assembly Chloroplast-genome-assembly-and-annotation Jan 22, 2025 3 ❌ ❌ ❌
De Bruijn Graph Assembly Debruijn Graph Jan 22, 2025 4 ✅ ❌ ❌
Decontamination of a genome assembly Assembly-decontamination-VGP9 Jan 22, 2025 1 ✅ ✅ ❌
ERGA post-assembly QC Post-assembly workflow Jan 22, 2025 2 ✅ ✅ ❌
Genome Assembly Quality Control Genome Assembly Quality Control Jan 22, 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) Jan 22, 2025 1 ✅ ❌ ❌
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data Genome Assembly of MRSA using Illumina MiSeq Data Jan 22, 2025 2 ✅ ❌ ❌
Genome assembly using PacBio data Genome Assembly using PacBio data Jan 22, 2025 1 ❌ ❌ ❌
Large genome assembly and polishing Assembly polishing - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assembly with Flye - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Assess genome quality - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Combined workflows for large genome assembly - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Data QC - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Racon polish with Illumina reads (R1 only), x2 - upgraded Jan 22, 2025 2 ❌ ❌ ❌
Large genome assembly and polishing Racon polish with long reads, x4 - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing Trim and filter reads - fastp - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Large genome assembly and polishing kmer counting - meryl - upgraded Jan 22, 2025 2 ❌ ✅ ❌
Making sense of a newly assembled genome Ecoli Comparison Jan 22, 2025 3 ❌ ❌ ❌
Unicycler Assembly Unicycler training Jan 22, 2025 4 ✅ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing Jan 22, 2025 1 ❌ ❌ ❌
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads assembly_with_preprocessing_and_sra_download Jan 22, 2025 1 ❌ ❌ ❌
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step VGP assembly: training workflow Jan 22, 2025 4 ❌ ❌ ❌

Your topic's Workflow Testing Results

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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 introcuction sequence-analysis assembly
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Events using materials from this Topic

TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963

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