De novo assembly pipeline for 10X linked-reads using Supernova
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1yr ago
Version:
1.0.0
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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
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:
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 .
Code Snippets
245 246 247 | """ supernova run --id=${id} --fastqs=${fastqs} ${tenx_options} ${supernova_options} """ |
266 267 268 269 270 271 272 273 | """ supernova run --id=${id} --fastqs=${fastqs} ${tenx_options} ${supernova_options} rsync -rav --include="_*" --include="*.tgz" --include="outs/" --include="outs/*.*" \ --include="assembly/" --include="stats/***" --include="logs/***" --include="a.base/" \ --include="a.base/" --include="a.hbx" --include="a.inv" --include="final/***" --include="gang" \ --include="micro" --include="a.hbx" --include="a.inv" --include="final/***" \ --exclude="*" "${id}/" ${id}_supernova """ |
291 292 293 294 | """ supernova mkoutput --asmdir=${id}_supernova/outs/assembly --outprefix=${id} --style=pseudohap --minsize=${params.minsize} --nozip supernova mkoutput --asmdir=${id}_supernova/outs/assembly --outprefix=${id}.phased --style=megabubbles --minsize=${params.minsize} --nozip """ |
309 310 311 | """ quast.py ${size_parameter} --threads ${task.cpus} ${asm} """ |
327 328 329 330 331 | """ tar xfj ${augustus_archive} export AUGUSTUS_CONFIG_PATH=augustus_config/ run_BUSCO.py -i ${asm} -o ${id} -c ${task.cpus} -m genome -l ${buscoPath} """ |
340 341 342 | """ supernova run --version > v_supernova.txt """ |
359 360 361 362 363 364 365 366 | """ echo $workflow.manifest.version > v_pipeline.txt echo $workflow.nextflow.version > v_nextflow.txt quast.py -v &> v_quast.txt multiqc --version > v_multiqc.txt run_BUSCO.py -v > v_busco.txt scrape_software_versions.py &> software_versions_mqc.yaml """ |
384 385 386 | """ multiqc -i ${custom_runName} -f -s --config ${mqc_config} . """ |
399 400 401 | """ markdown_to_html.r $output_docs results_description.html """ |
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