gene-fusions-nf

A nextflow pipeline to call somatic rna fusions from RNA-seq data using arriba

Dependencies

1. Nextflow : for common installation procedures see the IARC-nf repository.
2. arriba

A conda receipe, and docker and singularity containers are available with all the tools needed to run the pipeline (see "Usage")

Input

Type	Description
reads	Path to input data
bams	Path to folder containing BAM files for processing

Parameters

• Mandatory

Name	Example value	Description
ref_fa	ref.fa	Path to fasta reference
ref_gtf	annot.gtf	Path to GTF annotation
star_index	index/	Path to STAR-Index reference

• Optional

Name	Default value	Description
reads_csv	NULL	file with tabular data for each sample to process
svs	NULL	file with tabular data for each sample with structural variants in bedpe format

• Flags

Flags are special parameters without value.

Name	Description
--arriba_plot	by default plot all the gene fusions detected by arriba. set to false to deactivate
--help	Display help

Usage

nextflow run  iarc/nf-gene-fusions -r v1.1 -profile singularity --reads 'test_dataset/reads/*.R{1,2}.fastq.gz' --ref_fa test_dataset/genome.fa --ref_gtf test_dataset/genome.gtf

  or

nextflow run  iarc/nf-gene-fusions -r v1.1 -profile singularity --bams '/path/to/bams/' --ref_fa test_dataset/genome.fa --ref_gtf test_dataset/genome.gtf

To run the pipeline without singularity just remove "-profile singularity". Alternatively, one can run the pipeline using a docker container (-profile docker) the conda receipe containing all required dependencies (-profile conda).

Output

Type	Description
outdir	Folder with fusion genes file

Contributions

Name	Email	Description
Alex Di Genova		Developer

References

Sebastian Uhrig, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H. Toprak, Olaf Neumann, Albrecht Stenzinger, Claudia Scholl, Stefan Fröhling and Benedikt Brors: Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research. March 2021 31: 448-460; Published in Advance January 13, 2021. doi: 10.1101/gr.257246.119