nfcore/neutronstar repository overview

De novo assembly pipeline for 10X linked-reads.

⁠⚠️ Important note

Due to the discontinuation of the primary data source (10X Chromium) for this pipeline, it is now archived. This means that it will no longer be updated.

⁠Table of Contents

1. Introduction⁠
   • Disclaimer⁠
2. Important installation information⁠
   • Singularity⁠
   • Busco data⁠
3. Usage instructions⁠
   • Single assembly⁠
   • Multiple assemblies⁠
   • Advanced usage⁠
4. Pipeline output⁠
5. Pipeline overview⁠
6. Credits⁠

⁠Introduction

nf-core/neutronstar is a bioinformatics best-practice analysis pipeline used for de-novo assembly and quality-control of 10x Genomics Chromium data. The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

⁠Quick Start

i. Install nextflow⁠

ii. Install one of docker⁠, singularity⁠ or conda⁠

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/neutronstar -profile test,<docker/singularity/conda>

iv. Start running your own analysis!

nextflow run nf-core/neutronstar -profile <docker/singularity/conda> --id assembly_id --fastqs fastq_path --genomesize 1000000

See usage docs⁠ for all of the available options when running the pipeline.

⁠Disclaimer

This software is in no way affiliated with nor endorsed by 10x Genomics.

⁠Pipeline overview

⁠Credits

nf-core/neutronstar was originally written by Remi-Andre Olsen (@remiolsen).

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch on Slack⁠ (you can join with this invite⁠).

⁠Citation

If you use nf-core/neutronstar for your analysis, please cite it using the following doi:

You can cite the nf-core pre-print as follows: