nf-core pipeline · dualrna-seq, host-pathogen, quantification
nf-core/dualrnaseq
Simultaneous analysis of host and pathogen gene expression from dual RNA-seq sequencing data.
What nf-core/dualrnaseq is
nf-core/dualrnaseq is a Nextflow bioinformatics pipeline developed by Bozena Mika-Gospodorz and Regan Hayward for the analysis of dual RNA-seq experiments. Dual RNA-seq is an experimental approach that sequences the transcriptomes of both a host and an infecting pathogen simultaneously, allowing researchers to study their interaction dynamics during infection.
Analysing mixed transcriptomes presents unique challenges, as reads originate from two disparate organisms with distinct genome structures and annotation formats. The pipeline was initially tested using human and mouse eukaryotic hosts alongside bacterial pathogens including Salmonella enterica, Orientia tsutsugamushi, Streptococcus pneumoniae, Escherichia coli, and Mycobacterium leprae, but it supports any eukaryotic and bacterial pairing with available reference genomes and annotations.
What the pipeline does
The pipeline begins by merging the host and pathogen reference genome annotations, adjusting for differing annotation conventions between eukaryotic and bacterial formats. Raw sequencing data supplied in FASTQ format undergo quality control and read trimming using FastQC and BBDuk.
For expression quantification, the pipeline offers three distinct routes: STAR alignment combined with HTSeq; STAR alignment combined with Salmon and tximport; or Salmon in quasimapping mode followed by tximport. Finally, overall run metrics are aggregated via MultiQC, and the pipeline generates dedicated summary plots along with distinct, segregated result tables for the host and the pathogen.
Key facts
- Workflow manager
- Nextflow
- Pipeline authors
- Bozena Mika-Gospodorz and Regan Hayward
- Version
- 1.0.0
- Primary input format
- FASTQ
- Quality control and trimming
- FastQC, BBDuk
- Alignment and quantification tools
- STAR, HTSeq, Salmon, tximport
- Reporting tools
- MultiQC
- Tested eukaryotic hosts
- Human, Mouse
- Tested bacterial pathogens
- Salmonella enterica, Orientia tsutsugamushi, Streptococcus pneumoniae, Escherichia coli, Mycobacterium leprae
What you can use it for
- Simultaneous host-pathogen transcriptomic profiling
- Quantifying concurrent gene expression changes in infected host tissues and internalized or associated bacteria from a single RNA sequencing run.
- Bacterial infection studies
- Evaluating the transcriptional responses of bacterial pathogens like S. enterica, S. pneumoniae, or M. leprae during active eukaryotic host colonization.
- Flexible expression quantification
- Benchmarking or selecting between alignment-based counting (STAR with HTSeq or Salmon) and pseudo-alignment (Salmon quasimapping mode) across combined genomes.
Run it here
The research agent runs nf-core/dualrnaseq with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Merges host and pathogen reference annotations while resolving differences in annotation conventions between organism types.
- Provides three alternative quantification workflows spanning STAR, HTSeq, Salmon, and tximport.
- Outputs separate, clear results tables and custom summary visualisations for host and pathogen transcriptomes.
- Accommodates any eukaryotic host and bacterial pathogen pairing provided reference sequences and annotations are available.
Watch out for
- Requires existing reference genomes and annotation files for both the host and pathogen organisms.
- Designed specifically for eukaryotic host and bacterial pathogen systems rather than viral or complex multi-species communities.
Questions
Can I run nf-core/dualrnaseq without my own cluster?
The research agent runs nf-core/dualrnaseq with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/dualrnaseq under?
MIT, like every nf-core pipeline.
Which organism pairs can this pipeline process?
The pipeline is designed for any eukaryotic host and bacterial pathogen with available reference genomes and annotations. It has been tested with human and mouse hosts against pathogens such as Salmonella enterica, Orientia tsutsugamushi, Streptococcus pneumoniae, Escherichia coli, and Mycobacterium leprae.
What alignment and quantification options are available?
The pipeline supports three quantification workflows: STAR alignment paired with HTSeq counting; STAR alignment with Salmon and tximport; or Salmon in quasimapping mode coupled with tximport.
How does the pipeline handle separate host and pathogen annotations?
It automatically integrates the host and pathogen genome annotations prior to read mapping, accounting for discrepancies in standard annotation conventions between eukaryotic and bacterial species.
What outputs are provided?
The pipeline outputs MultiQC quality reports, custom summary plots, and segregated expression result tables for the host and the pathogen.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/dualrnaseq's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.