nf-core pipeline · ortholog
nf-core/reportho
Comparative analysis and consensus aggregation of orthologue predictions for protein queries.
What nf-core/reportho is
nf-core/reportho is a bioinformatics pipeline designed to compare and summarise orthology predictions for single or multiple query proteins. Originally written by Igor Trujnara, the workflow addresses discrepancies between public orthology repositories by collating predictions, reconciling synonymous identifiers, and calculating agreement metrics.
By compiling data across databases via programmatic interfaces or local snapshots, the pipeline establishes a consensus list of orthologues filtered to a chosen confidence level. It produces structured data summaries and an interactive HTML report to assist researchers in evaluating orthology relationships across species.
What the pipeline does
The workflow begins by determining the UniProt identifier and taxonomy identifier for each query protein. If a FASTA file is supplied instead of an accession, the pipeline identifies the closest annotated homologue. Orthologue lists are subsequently retrieved from public databases using remote APIs or local database snapshots.
Unless bypassed with the skip merge option, the pipeline downloads the identified orthologue sequences and merges synonymous identifiers based on sequence identity. Pairwise and global agreement scores are calculated across predictions, a consensus orthologue list matching the chosen confidence threshold is assembled, and an HTML report is produced.
Key facts
- Pipeline engine
- Nextflow (nf-core)
- Latest release
- 1.1.0
- Lead developer
- Igor Trujnara
- Input formats
- CSV samplesheet with UniProt IDs or FASTA files
- Data acquisition
- Database APIs or local snapshot files
- Primary outputs
- Consensus orthologue lists, agreement metrics, and HTML report
What you can use it for
- Cross-database orthologue aggregation
- Retrieve and compare orthology assignments from multiple public resources for target protein queries.
- High-confidence orthologue filtering
- Derive consensus lists of orthologous proteins using global and pairwise database agreement metrics.
- Sequence-based orthology querying
- Infer orthologues for novel protein sequences in FASTA format by identifying their nearest annotated homologue.
Run it here
The research agent runs nf-core/reportho 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
- Resolves redundant or differing identifiers across databases by clustering identical protein sequences.
- Calculates both pairwise and global agreement scores across disparate orthology databases.
- Supports both live API queries and offline local snapshot files for orthologue collection.
- Produces a human-readable HTML summary report of orthology predictions and metrics.
Watch out for
- The current version is not tested with Conda due to an external nf-test issue.
- When both a UniProt identifier and a FASTA file are provided for a sample, the pipeline prioritises the UniProt ID and ignores the FASTA file.
Questions
Can I run nf-core/reportho without my own cluster?
The research agent runs nf-core/reportho 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/reportho under?
MIT, like every nf-core pipeline.
What inputs are accepted by nf-core/reportho?
The pipeline accepts a CSV samplesheet containing protein identifiers, which can be supplied as either UniProt accession numbers or paths to FASTA sequence files.
Can the pipeline be run without internet access?
Yes, orthologue predictions can be fetched from local snapshot files rather than public database APIs.
Can sequence retrieval and identifier merging be disabled?
Yes, sequence retrieval and the sequence-identity merging of synonymous identifiers can be skipped using the --skip_merge parameter.
How does the pipeline process proteins supplied as FASTA files?
It identifies the closest annotated homologue to retrieve the necessary UniProt identifier and taxon identifier before querying orthology resources.
How to cite it
doi: 10.5281/zenodo.11574565
Written from nf-core/reportho's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.