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.
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.
This software is in no way affiliated with nor endorsed by 10x Genomics.
nf-core/neutronstar was originally written by Remi-Andre Olsen (@remiolsen).
If you would like to contribute to this pipeline, please see the contributing guidelines.
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:
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.