Assembly

🎥 Recording of Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads

2026-04-03T00:00:00+00:00

A 2H46M long recording is now available.

🎥 Recording of Assembly of metagenomic sequencing data

2026-03-26T00:00:00+00:00

A 1H15M long recording is now available.

📅 Galaxy Training Academy 2026

Delphine Lariviere — 2026-01-21T17:14:51+00:00

The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their data analysis skills in Galaxy and/or in popular fields in bioinformatics. Over the course of one week, we offer a diverse selection of learning tracks for you.

🛠️ Debruijn Graph Velvet Optimiser and SPAdes Assembly

2026-01-07T19:08:37+00:00

🛠️ Debruijn Graph Velvet Full and SPAdes Assembly

2026-01-07T19:08:37+00:00

🛠️ Debruijn Graph SPAdes Assembly

2026-01-07T19:08:37+00:00

📚 Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads

2025-12-18T12:43:50+00:00

Metagenomics has revolutionized our understanding of microbial communities by enabling the study of genetic material directly from environmental samples. One of the most powerful applications of metagenomics is the reconstruction of Metagenome-Assembled Genomes (MAGs), i.e. near-complete or complete genomes of individual microorganisms recovered from complex microbial communities. MAGs provide invaluable insights into microbial diversity, function, and ecology, without the need for laboratory cultivation.

🛠️ Hybrid Genome Assembly Tutorial Workflow

2025-11-03T09:40:11+00:00

Workflow for the Galaxy Training Network tutorial "Hybrid genome assembly - Nanopore and Illumina"

📚 Hybrid genome assembly - Nanopore and Illumina

2025-11-03T09:40:11+00:00

Assemble a genome! Learn how to create and assess genome assemblies using the powerful combination of Nanopore and Illumina reads.

🖼️ Genome assembly and assembly QC - Introduction short version

2025-04-22T12:37:09+00:00

Genome assembly

📅 Galaxy Training Academy 2025

Delphine Lariviere — 2025-02-10T19:40:45+00:00

The Galaxy Training Academy is a self-paced online training event for beginners and advanced learners who want to improve their Galaxy data analysis skills. Over the course of one week, we offer a diverse selection of learning track for you.

🎥 Recording of ERGA post-assembly QC

2024-10-06T00:00:00+00:00

A 44M long recording is now available.

🎥 Recording of Assembly of the mitochondrial genome from PacBio HiFi reads

2024-09-20T00:00:00+00:00

A 11M long recording is now available.

🎥 Recording of Decontamination of a genome assembly

2024-09-20T00:00:00+00:00

A 29M long recording is now available.

🎥 Recording of Chloroplast genome assembly

2024-09-12T00:00:00+00:00

A 16M long recording is now available.

🎥 Recording of Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data

2024-09-12T00:00:00+00:00

A 1H56M long recording is now available.

🛠️ Assembly-decontamination-VGP9

2024-09-04T10:07:40+00:00

📚 Decontamination of a genome assembly

2024-09-04T10:07:40+00:00

When sequencing a genome, it is common that contamination from a foreign organism get mixed with the genomic material of our species of interest. For instance, if you are processing a whole body sample of an insect then you will sequence not only the insect, but everything on and inside of it. When building a reference genome, it is important to separate these contaminants from the genome of our species. Foreign DNA sequences could cause false positive identification when running BLAST analyses, the misidentification of genes that don’t actually belong to the species, or they can be incorporated as ‘reference’ sequence for that species in the public archives when those sequences did not actually belong to that species.

🎥 Recording of Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

2024-09-04T00:00:00+00:00

A 39M long recording is now available.

🛠️ Mitogenome-Assembly-VGP0

2024-09-03T07:08:55+00:00

📚 Assembly of the mitochondrial genome from PacBio HiFi reads

2024-09-03T07:08:55+00:00

This tutorial will show you how to assemble a mitochondrial genome from PacBio HiFi data using MitoHiFi Uliano-Silva et al. 2023.

📅 Galaxy Training Academy 2024

Teresa Müller — 2024-06-11T15:07:31+00:00

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.

🛠️ Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)

2024-03-04T11:13:27+00:00

Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

❓ Upload fasta datasets via links

2023-11-27T17:09:50+00:00

🛠️ Post-assembly workflow

2023-06-23T16:06:20+00:00

ERGA post-assembly QC

📚 ERGA post-assembly QC

2023-06-23T16:06:20+00:00

🎥 Recording of Large genome assembly and polishing

2023-05-16T00:00:00+00:00

A 25M long recording is now available.

🎥 Recording of Assembly of metagenomic sequencing data

2023-05-02T00:00:00+00:00

A 1H long recording is now available.

🛤️ Introduction to Galaxy and Sequence analysis

2023-04-13T15:51:25+00:00

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.

🛠️ kmer counting - meryl - upgraded

2023-03-06T16:02:30+00:00

🛠️ Trim and filter reads - fastp - upgraded

2023-03-06T16:02:30+00:00

🛠️ Racon polish with long reads, x4 - upgraded

2023-03-06T16:02:30+00:00

🛠️ Racon polish with Illumina reads (R1 only), x2 - upgraded

2023-03-06T16:02:30+00:00

🛠️ Data QC - upgraded

2023-03-06T16:02:30+00:00

🛠️ Combined workflows for large genome assembly - upgraded

2023-03-06T16:02:30+00:00

🛠️ Assess genome quality - upgraded

2023-03-06T16:02:30+00:00

🛠️ Assembly with Flye - upgraded

2023-03-06T16:02:30+00:00

🛠️ Assembly polishing - upgraded

2023-03-06T16:02:30+00:00

📚 Large genome assembly and polishing

2023-03-06T16:02:30+00:00

Note: We recommend running this tutorial on either the Galaxy Europe or Galaxy Australia servers. Other servers (such as Galaxy main) have not yet been configured fully for all the tools in this analysis.

📚 Assembly of metagenomic sequencing data

2022-12-05T10:09:59+00:00

Metagenomics involves the extraction, sequencing and analysis of combined genomic DNA from entire microbiome samples. It includes then DNA from many different organisms, with different taxonomic background.

🛠️ Genome Assembly Quality Control

2022-08-26T14:11:00+00:00

Genome assembly quality control using PacBio data and with reference genome

🖼️ Genome assembly quality control.

2022-08-26T14:11:00+00:00

Genome assembly quality control, or “the 3C”

📚 Genome Assembly Quality Control

2022-08-26T14:11:00+00:00

In this tutorial, we will assess the assembly quality of 2 assemblies generated with Hifiasm and Flye using PacBio HiFi reads of a species of fungi, Saccharomyces cerevisiae INSC1019 and compare the results with the actual reference genome Saccharomyces cerevisiae S288C.

📚 Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data

2022-04-06T05:32:19+00:00

The Vertebrate Genome Project (VGP), a project of the Genome 10K (G10K) Consortium, aims to generate high-quality, near error-free, gap-free, chromosome-level, haplotype-phased, annotated reference genome assemblies for every vertebrate species (Rhie et al. 2020). The VGP has developed a fully automated de-novo genome assembly pipeline, which uses a combination of three different technologies: Pacbio high fidelity reads (HiFi), all-versus-all chromatin conformation capture (Hi-C) data, and (optionally) Bionano optical map data. The pipeline consists of nine distinct workflows. This tutorial provides a quick example of how to run these workflows for one particular scenario, which is, based on our experience, the most common: assembling genomes using HiFi Reads combined with Hi-C data (both generated from the same individual).

📰 New Tutorial: VGP assembly pipeline

2022-03-14T00:00:00+00:00

We are proud to announce that, as result of the collaboration with the Vertebrate Genomes Project (VGP), a new training describing the VGP assembly pipeline is now available in the Galaxy Training Network. The Vertebrate Genomes Project aims to generate high-quality, near-error-free, gap-free, chromosome-level, haplotype-phased, annotated reference genome assemblies for every vertebrate species.

🎥 Recording of Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

2022-03-13T00:00:00+00:00

A 10M long recording is now available.

❓ Downloading the files from the NCBI server fails or takes too long.

2022-03-02T15:46:20+00:00

Download the data from Zenodo instead (see overview box at top of tutorial). This method uses Galaxy’s generic data import functionality, and is more reliable and faster than the download from NCBI.

❓ Can we polish the assembly with long reads too?

2022-03-02T15:46:20+00:00

Yes. In this tutorial, we only polish the assembly with the short reads. This may be enough for bacterial genomes. However, for an even better polish (usually), a common approach is to also polish the assembly with the long reads. A typical workflow for this would assemble with long reads, then polish with long reads (x 4 rounds, with Racon), polish with long reads again (x 1 round, with Medaka), then polish with short reads (x2 rounds with Pilon).

❓ Running more than one round of Pilon polishing

2022-03-02T15:46:20+00:00

❓ Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?

2022-03-02T15:46:20+00:00

In our experience, when both long and short reads are allowed as input, the difference comes down to the order in which set is assembled first. For example, Unicycler assembles the short reads first (which can be good, because they are more accurate), and then scaffolds these into larger contigs using long reads. Other tools (or workflows) often assemble long reads first (which can also be good because these can span repeat regions), then correct this assembly with information from the more accurate short reads. There may also be other variations on long/short read assembly, and/or iterations of these types of steps (assemble, correct). My preference is to assemble long reads first, but that’s because I’m really interested in covering repeat regions. If accuracy was the aim, rather than contig length, the short-reads-first approach may be better. For even more complexity … I think some tools now allow input of “trusted contigs” - i.e. contigs assembled from other tools. Ryan Wick has a new tool called Trycyler that can take in multiple assemblies to make a consensus (bacterial genomes).

❓ Why does my assembly graph in Bandage look different to the one pictured in the tutorial?

2022-03-02T15:46:20+00:00

The assembly process in Flye is heuristic, and the resulting assembly will not necessarily be exactly the same each time. This may happen even if running the same data with the same version of Flye. It can also happen with a different version of Flye.

❓ Is it possible to use alternative tools to those proposed in the tutorial?

2022-03-02T15:46:20+00:00

Yes! There are many tools whose functionality are similar (e.g. Illumina reads can be mapped by using HISAT2 instead of Bowtie2).

📰 New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate

2021-12-01T00:00:00+00:00

We have just finished a new collection of training material for genome assembly and annotation! You now have access to slides and tutorials, focused on the complete analysis of the genome of a fungus species (Mucor mucedo).

🖼️ An introduction to get started in genome assembly and annotation

2021-11-30T21:54:19+00:00

The truth about bioinformatics

🛠️ Genome Assembly using PacBio data

2021-11-29T14:55:42+00:00

Genome Assembly using PacBio data and Flye or Hifiasm assembler

📚 Genome assembly using PacBio data

2021-11-29T14:55:42+00:00

In this tutorial, we will assemble a genome of a species of fungi in the family Aspergillus, Aspergillus niger, from PacBio sequencing data. These data will be downloaded from ENA. The quality of the assembly obtained will be analyzed, in particular by comparing it to a reference assembly, available on ENA.

❓ Upload fastqsanger datasets via links

2021-08-04T19:00:46+00:00

🛠️ VGP assembly: training workflow

2021-06-04T07:34:12+00:00

VGP assembly tutorial

📚 Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

2021-06-04T07:34:12+00:00

Advances in sequencing technologies over the last few decades have revolutionized the field of genomics, allowing for a reduction in both the time and resources required to perform de novo genome assembly. Until recently, second-generation sequencing technologies (also known as next generation sequencing (NGS)) produced highly accurate but short (up to 800bp) reads. These read lengths were not long enough to cope with the difficulties associated with repetitive regions. Today, so-called third-generation sequencing (TGS) technologies, also known as single-molecule real-time (SMRT) sequencing, have become dominant in de novo assembly of large genomes. TGS can use native DNA without amplification, reducing sequencing error and bias (Hon et al. 2020, Giani et al. 2020). In 2020, PacBio introduced high fidelity (HiFi) sequencing, which produces reads 10-25 kbp in length with a minimum accuracy of 99% (Q20). In this tutorial, you will use HiFi reads in combination with data from additional sequencing technologies to generate a high-quality genome assembly.

🛠️ Genome Assembly of MRSA using Illumina MiSeq Data

2021-03-24T18:30:46+00:00

Genome Assembly of MRSA using Illumina MiSeq Data

📚 Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

2021-03-24T18:30:46+00:00

Sequencing (determining of DNA/RNA nucleotide sequence) is used all over

📚 Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

2021-03-24T18:30:46+00:00

Sequencing (determining of DNA/RNA nucleotide sequence) is used all over

📰 New Tutorials: Genome assembly of a MRSA genome

2021-03-24T00:00:00+00:00

Two new assembly tutorials have been added to the GTN! These tutorials walk you through the

🎥 Recording of Chloroplast genome assembly

2021-02-15T00:00:00+00:00

A 35M long recording is now available.

🎥 Recording of Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

2021-02-15T00:00:00+00:00

A 25M long recording is now available.

🎥 Recording of Antibiotic resistance detection

2021-02-15T00:00:00+00:00

A 45M long recording is now available.

🎥 Recording of An Introduction to Genome Assembly

2021-02-15T00:00:00+00:00

A 25M long recording is now available.

🛠️ Chloroplast-genome-assembly-and-annotation

2021-01-27T10:23:44+00:00

Assembly

🖼️ Deeper look into Genome Assembly algorithms

2021-01-12T13:46:54+00:00

Different types of input data

🖼️ Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

2021-01-07T10:02:09+00:00

.enlarge120[

📚 Chloroplast genome assembly

2020-12-04T09:03:20+00:00

What is genome assembly?

🛠️ assembly_with_preprocessing_and_sra_download

2020-04-22T12:48:44+00:00

Assembly with preprocessing and SRA download

🛠️ assembly_with_preprocessing

2020-04-22T12:48:44+00:00

Assembly with preprocessing

📚 Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

2020-04-21T21:52:12+00:00

In some research or clinical contexts it is not possible, or very hard, to

📚 Antibiotic resistance detection

2019-06-25T20:28:00+00:00

Overview

🛠️ Ecoli Comparison

2019-02-14T07:43:54+00:00

Making sense of a newly assembled genome

🛠️ Unicycler training

2018-08-24T15:43:31+00:00

Unicycler Assembly

📚 Making sense of a newly assembled genome

2018-06-14T14:42:30+00:00

In this tutorial we begin with a new genome assembly just produced in the Unicycler tutorial. This is an assembly of E. coli C, which we will be comparing to assemblies of all other complete genes of this species.

🖼️ Unicycler Assembly

2017-10-11T15:24:22+00:00

Small Genome Assembly With Unicycler

📚 Unicycler Assembly

2017-10-11T15:24:22+00:00

The goal: E. coli C-1 assembly

🖼️ An Introduction to Genome Assembly

2017-06-23T13:31:58+00:00

.enlarge120[

🛠️ Intro to Genome Assembly

2017-06-23T08:02:56+00:00

tutorial

🖼️ De Bruijn Graph Assembly

2017-05-24T15:42:44+00:00

.enlarge120[

📚 De Bruijn Graph Assembly

2017-05-24T15:42:44+00:00

Optimised de Bruijn Graph assemblies using the Velvet Optimiser and SPAdes

📚 An Introduction to Genome Assembly

2017-05-23T16:37:24+00:00

Genome assembly with Velvet: Background