nf-core pipeline · genome-assembly
nf-core/genomeassembler
Assembles, polishes, and scaffolds haploid or unphased genomes from Oxford Nanopore or PacBio HiFi sequencing reads.
What nf-core/genomeassembler is
nf-core/genomeassembler is a bioinformatics pipeline designed for the de novo assembly, polishing, and scaffolding of haploid or unphased genomes. It processes long-read sequencing data generated by Oxford Nanopore Technologies (ONT) or Pacific Biosciences (PacBio) HiFi platforms.
The pipeline was developed and is maintained by Niklas Schandry at the Ludwig-Maximilians University (LMU) in Munich, Germany, with support from the German Research Foundation (DFG). It provides a standard workflow integrating multiple assemblers, error-correction tools, and scaffolding options.
By combining various assembly, scaffolding, and quality-control utilities, the workflow enables scientists to generate and evaluate genome assemblies without manually chaining independent software packages.
What the pipeline does
The pipeline performs de novo assembly on long ONT or PacBio HiFi reads using Flye, Hifiasm, or a combination of both. Optional post-assembly polishing can be executed using Medaka for ONT reads, Dorado (marked as experimental and limited to ONT), or Pilon when Illumina short-read data are provided.
Contigs can be scaffolded using long reads with LINKS or Longstitch, chromosome conformation data with YaHS when Hi-C reads are provided, or an existing reference genome using RagTag. Quality evaluation is carried out across the workflow using BUSCO to evaluate gene completeness, QUAST for assembly statistics, and Merqury for k-mer analysis if short reads are supplied.
Key facts
- Pipeline engine
- Nextflow
- Latest release
- 1.1.0
- Assembly software
- Flye, Hifiasm
- Polishing software
- Medaka, Dorado, Pilon
- Scaffolding software
- LINKS, Longstitch, YaHS, RagTag
- Quality control tools
- BUSCO, QUAST, Merqury
- Primary inputs
- ONT or PacBio HiFi long reads (optional short reads and Hi-C reads)
What you can use it for
- De novo long-read assembly
- Assemble haploid or unphased genomes from long ONT or PacBio HiFi data using Flye, Hifiasm, or both.
- Hi-C chromosome scaffolding
- Scaffold newly assembled contigs into higher-order assemblies using YaHS when paired Hi-C sequencing reads are available.
- Reference-guided scaffolding
- Order and orient contigs against an existing related genome assembly using RagTag.
- Short-read polishing and k-mer evaluation
- Correct base-level errors using Pilon and benchmark assembly quality using Merqury when complementary short-read sequencing is provided.
Run it here
The research agent runs nf-core/genomeassembler 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.
Strengths and limits
Good at
- Supports multiple assembly tools, including Flye, Hifiasm, and combinations of both.
- Provides varied scaffolding routes using long reads (LINKS, Longstitch), Hi-C data (YaHS), or reference genomes (RagTag).
- Integrates standard quality control packages including BUSCO, QUAST, and Merqury.
Watch out for
- Does not support the phasing of polyploid genomes.
- Dorado polishing is experimental and restricted to ONT reads.
- Pilon polishing and Merqury quality evaluation depend on the availability of short-read data.
Questions
Can I run nf-core/genomeassembler without my own cluster?
The research agent runs nf-core/genomeassembler 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/genomeassembler under?
MIT, like every nf-core pipeline.
Which sequencing technologies are supported for initial assembly?
The pipeline is designed to work with long reads from Oxford Nanopore Technologies (ONT) or PacBio HiFi platforms.
Can this pipeline assemble polyploid organisms into phased haplotypes?
No, the pipeline currently does not implement phasing for polyploid genomes and is intended for haploid or unphased data.
Are short reads required to run the pipeline?
Short reads are not mandatory for basic assembly and scaffolding, but they are required if you want to perform polishing with Pilon or k-mer quality evaluation with Merqury.
What options exist for scaffolding assemblies?
Assemblies can be scaffolded using long reads via LINKS or Longstitch, Hi-C reads via YaHS, or an existing reference genome using RagTag.
How to cite it
10.5281/zenodo.14986998
Written from nf-core/genomeassembler's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.