Nextflow rnafusion analysis pipeline, part of the nf-core community..
nf-core/rnafusion is a bioinformatics best-practise analysis pipeline for identifying gene fusions from RNA-seq experiments.
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.
Tool | Single-end reads | Version |
---|---|---|
Arriba | ❌ | 1.2.0 |
EricScript | ❌ | 0.5.5 |
FusionCatcher | ✅ | 1.20 |
Fusion-Inspector | ❌ | 2.3.1 |
fusion-report | - | 2.1.3 |
Pizzly | ❌ | 0.37.3 |
Squid | ❌ | 1.5 |
Star-Fusion | ✅ | 1.9.1 |
-
Install
nextflow
-
Install any of
Docker
,Singularity
orPodman
for full pipeline reproducibility (please only useConda
as a last resort; see docs) -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run nf-core/rnafusion -profile test,<docker/singularity/podman/conda/institute>
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>
in your command. This will enable eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. -
Start running your own analysis!
nextflow run nf-core/rnafusion -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
See usage docs for all of the available options when running the pipeline.
By default, the pipeline currently performs the following:
- Sequencing quality control (
FastQC
) - Overall pipeline run summaries (
MultiQC
)
The nf-core/rnafusion pipeline comes with documentation about the pipeline: usage and output.
nf-core/rnafusion was originally written by Martin Proks.
We thank the following people for their extensive assistance in the development of this pipeline:
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 the Slack #rnafusion
channel (you can join with this invite).
You can cite the nf-core
publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link
In addition, references of tools and data used in this pipeline are as follows: