README.md

Introduction

nf-core/reportho is a bioinformatics pipeline that compares and summarizes orthology predictions for one or a set of query proteins. For each query (or its closest annotated homolog), it fetches ortholog lists from public databases, calculates the agreement of the obtained predictions(pairwise and global) and finally generates a consensus list of orthologs 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.

1. Obtain Query Information: identification of Uniprot ID and taxon ID for the query (or its closest homolog if the fasta file is used as input instead of the Uniprot ID).
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.

4. Fetch Sequences: fetching of protein sequences for the orthologs from Uniprot.
5. Fetch Structures: fetching of protein structure from the AlphaFold Database. Only performed if --use_structures is true.
6. Align Sequences: multiple sequence alignment. 3D-COFFEE is used if --use_structures is true, T-COFFEE otherwise.
7. Reconstruct Phylogeny: character-based phylogenetic reconstruction with ML or ME. Only performed if at least one of --use_iqtree or --use_fastme is true.
8. 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:

id,fasta
BicD2,data/bicd2.fasta
HBB,data/hbb.fasta

or if you know the UniProt ID of the protein you can provide it directly:

id,query
BicD2,Q8TD16
HBB,P68871

Note

If you provide both a FASTA file and a UniProt ID only the latter will be used.

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.

Report image

The code to create the image producing the pipeline report is available under this GitHub repository.

Credits

nf-core/reportho was originally written by Igor Trujnara (@itrujnara).

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

• Luisa Santus (@luisas)
• Alessio Vignoli (@alessiovignoli)
• Jose Espinosa-Carrasco (@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.