Introduction

Warning

This pipeline is still in active development. While the overall design will remain stable, all technical details, such as parameter names, are subject to change without notice.

nf-core/reportho is a bioinformatics pipeline that compares and assembles orthology predictions for a query protein. It fetches ortholog lists for a query (or its closest annotated homolog) from public sources, calculates pairwise and global agreement, and generates a consensus list with the desired level of confidence. Optionally, it offers common analysis on the consensus orthologs, such as MSA and phylogeny reconstruction. Additionally, it generates a clean, human-readable report of the results.

nf-core-reportho tube map

  1. Obtain Query Information: (depends on provided input) identification of Uniprot ID and taxon ID for the query or its closest homolog.
  2. Fetch Orthologs: fetching of ortholog predictions from public databases, either through API or from local snapshot.
  3. Compare and Assemble: calculation of agreement statistics, creation of ortholog lists, selection of the consensus list.

Steps that follow can be skipped with --skip_downstream in batch analysis.

  1. Fetch Sequences: fetching of protein sequences for the orthologs from Uniprot.
  2. Fetch Structures: fetching of protein structure from the AlphaFold Database. Only performed if --use_structures is true.
  3. Align Sequences: multiple sequence alignment. 3D-COFFEE is used if --use_structures is true, T-COFFEE otherwise.
  4. Reconstruct Phylogeny: character-based phylogenetic reconstruction with ML or ME. Only performed if at least one of --use_iqtree or --use_fastme is true.
  5. Generate Report: human-readable HTML report generation.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

id,query
BicD2,data/bicd2.fasta

or:

id,query
BicD2,Q8TD16

If using the latter format, you must set --uniprot_query to true.

Now, you can run the pipeline using:

nextflow run nf-core/reportho \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters;

see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/reportho was originally written by itrujnara.

We thank the following people for their extensive assistance in the development of this pipeline:

@lsantus

@avignoli

@JoseEspinosa

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 the Slack #reportho channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

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.