nf-core pipeline · archived · assembly, denovo, denovo-assembly
nf-core/denovohybrid
A bioinformatics pipeline for hybrid de novo genome assembly using long and short sequencing reads.
What nf-core/denovohybrid is
nf-core/denovohybrid is a genomic assembly pipeline designed to produce de novo genome assemblies by combining long-read and short-read sequencing data. It integrates long reads from Oxford Nanopore Technologies with short reads from Illumina technologies, but can also run in a long-read-only configuration when short reads are unavailable. The pipeline was originally developed by Caspar Groß.
The workflow is constructed using Nextflow and uses Docker containers to ensure portable execution and reproducible results across compute environments. The project is marked as archived and is no longer maintained.
What the pipeline does
The pipeline processes sequencing data by performing read preprocessing and quality control on input reads. It then executes de novo assembly using selected assembly tools, followed by quality assessment of the assembled sequences. Depending on the target organism and chosen method, it utilises Unicycler for bacterial genomes, or miniasm or wtdbg2 for eukaryotic samples. If short-read data are omitted, the workflow automatically generates an assembly using long reads alone.
Key facts
- Workflow framework
- Nextflow
- Status
- Archived — no longer maintained
- Long-read technology
- Oxford Nanopore Technologies
- Short-read technology
- Illumina
- Bacterial assembly tool
- Unicycler
- Eukaryotic assembly tools
- miniasm, wtdbg2
- Containerisation
- Docker
What you can use it for
- Bacterial hybrid genome assembly
- Assemble bacterial genomes using a combination of Oxford Nanopore long reads and Illumina short reads processed via Unicycler.
- Eukaryotic de novo assembly
- Construct eukaryotic genome assemblies from sequencing data using the miniasm or wtdbg2 assembly methods.
- Long-read-only genome assembly
- Generate assemblies using only Oxford Nanopore reads when complementary Illumina short reads are not provided.
Strengths and limits
Good at
- Supports both hybrid short- and long-read data as well as long-read-only inputs.
- Includes dedicated assembly methods tailored separately for bacterial and eukaryotic genomes.
- Incorporates quality control checks both before assembly on the raw reads and after assembly on the final sequences.
- Uses Docker containers within Nextflow to ensure reproducible results across different compute systems.
Watch out for
- The repository is archived and no longer actively maintained.
- Development remained under construction, with planned integrations for additional long-read assemblers such as Shasta, wengan, and Flye left incomplete.
Questions
Can I run nf-core/denovohybrid without my own cluster?
The research agent runs nf-core/denovohybrid with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/denovohybrid under?
MIT, like every nf-core pipeline.
Can the pipeline run without short-read Illumina data?
Yes. When no short-read data are provided, the workflow automatically produces an assembly using only long reads.
Which assemblers are available for bacterial and eukaryotic data?
The pipeline employs Unicycler for bacterial samples, and miniasm or wtdbg2 for eukaryotic samples.
What sequencing platforms are supported?
The pipeline is designed to combine long reads from Oxford Nanopore Technologies and short reads from Illumina technologies.
Is nf-core/denovohybrid still supported?
No, the repository is archived and is no longer maintained.
Written from nf-core/denovohybrid's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.