nf-core pipeline · archived · 10x-genomics, 10xgenomics, denovo-assembly
nf-core/neutronstar
De novo genome assembly and quality control pipeline for 10x Genomics linked-reads using Supernova.
What nf-core/neutronstar is
nf-core/neutronstar is a bioinformatics analysis pipeline designed for de novo genome assembly and quality control using 10x Genomics Chromium linked-read data. It provides an automated workflow based on the Supernova assembler, originally developed by Remi-Andre Olsen.
The pipeline was created to process linked-read datasets across different computing environments in a portable and reproducible manner using containerised software dependencies.
Following the discontinuation of the 10x Genomics Chromium linked-read technology, the pipeline has been archived and is no longer actively maintained or updated.
What the pipeline does
The workflow is implemented in Nextflow and ingests raw FASTQ files alongside a user-defined assembly identifier and target genome size. It coordinates de novo assembly through Supernova and performs downstream quality-control checks, including evaluations using BUSCO reference datasets.
Tasks are containerised using Docker, Singularity, or Conda environments, allowing the steps to execute across various compute infrastructures.
Key facts
- Pipeline engine
- Nextflow
- Core assembler
- Supernova
- Input data
- 10x Genomics Chromium linked-read FASTQ files
- Required parameters
- Sample ID, FASTQ path, and genome size
- Quality control tool
- BUSCO
- Original author
- Remi-Andre Olsen
- Latest release
- 1.0.0 (2019-12-12)
- Maintenance status
- Archived
What you can use it for
- De novo linked-read assembly
- Assembling novel genomes from 10x Genomics Chromium linked-read sequencing data using Supernova.
- Assembly quality assessment
- Evaluating the completeness and quality of assembled linked-read genomes against BUSCO datasets.
- Batch genome reconstruction
- Running single or multiple 10x Chromium genome assemblies systematically across compute clusters.
Strengths and limits
Good at
- Combines de novo assembly via Supernova with quality control in a single standardised workflow.
- Offers reproducible execution across diverse compute infrastructures using Nextflow and software containers.
- Supports both single-sample and multiple-sample assembly runs.
Watch out for
- The pipeline is archived and receives no future software updates or bug fixes.
- Strictly tied to 10x Genomics Chromium linked-reads, a sequencing format that has been discontinued.
- Not affiliated with or endorsed by 10x Genomics.
Questions
Can I run nf-core/neutronstar without my own cluster?
The research agent runs nf-core/neutronstar 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/neutronstar under?
MIT, like every nf-core pipeline.
Which genome assembler does the pipeline utilise?
The pipeline uses Supernova to perform de novo genome assembly on linked-reads.
What primary inputs are required to run the pipeline?
It requires the path to 10x Genomics FASTQ files, an assembly identifier, and an estimated genome size.
Why is the pipeline marked as archived?
It was archived because the primary sequencing technology it supports, 10x Chromium linked-reads, was discontinued by the manufacturer.
Does the pipeline evaluate assembly quality?
Yes, the pipeline includes quality-control analysis and incorporates BUSCO reference data to inspect assemblies.
How to cite it
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.
Written from nf-core/neutronstar's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.