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proteinfamilies

Generation and update of protein families

https://github.com/nf-core/proteinfamilies

Science Score: 57.0%

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    Found 10 DOI reference(s) in README
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    Low similarity (9.8%) to scientific vocabulary

Keywords

bioinformatics metagenomics nextflow nf-core pipeline protein-families proteomics workflow
Last synced: 6 months ago · JSON representation ·

Repository

Generation and update of protein families

Basic Info
Statistics
  • Stars: 18
  • Watchers: 191
  • Forks: 3
  • Open Issues: 4
  • Releases: 6
Topics
bioinformatics metagenomics nextflow nf-core pipeline protein-families proteomics workflow
Created over 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/proteinfamilies

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow nf-core template version run with conda run with docker run with singularity Launch on Seqera Platform

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Introduction

nf-core/proteinfamilies is a bioinformatics pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits.

nf-core/proteinfamilies workflow overview

Check quality

Generate input amino acid sequence statistics with (SeqKit)

Create families

  1. Cluster sequences (MMseqs2)
  2. Perform multiple sequence alignment (MSA) (FAMSA or mafft)
  3. Optionally, clip gap parts of the MSA (ClipKIT)
  4. Generate family HMMs and fish additional sequences into the family (hmmer)
  5. Optionally, remove redundant families by comparing family representative sequences against family models with (hmmer)
  6. Optionally, from the remaining families, remove in-family redundant sequences by strictly clustering with (MMseqs2) and keep cluster representatives
  7. Optionally, if in-family redundancy was not removed, reformat the .sto full MSAs to .fas with (HH-suite3)
  8. Present statistics for remaining/updated family size distributions and representative sequence lengths (MultiQC)

Update families

  1. Find which families to update by comparing the input sequences against existing family models with (hmmer)
  2. For non hit sequences continue with the above: A. Create families. For hit sequences and families continue to: 3
  3. Extract family sequences (SeqKit) and concatenate with filtered hit sequences of each family
  4. Optionally, remove in-family redundant sequences by strictly clustering with (MMseqs2) and keeping cluster representatives
  5. Perform multiple sequence alignment (MSA) (FAMSA or mafft)
  6. Optionally, clip gap parts of the MSA (ClipKIT)
  7. Update family HMM with (hmmer)

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:

csv sample,fasta,existing_hmms_to_update,existing_msas_to_update CONTROL_REP1,input/mgnifams_input_small.fa,,

Each row contains a fasta file with amino acid sequences (can be zipped or unzipped). Optionally, a row may contain tarball archives (tar.gz) of existing families' HMM and MSA folders, in order to be updated. In this case, the HMM and MSA files must be matching in numbers and in base filenames (not the extension). Hit families/sequences will be updated, while no hit sequences will create new families.

Now, you can run the pipeline using:

bash nextflow run nf-core/proteinfamilies \ -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/proteinfamilies was originally written by Evangelos Karatzas.

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

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 #proteinfamilies channel (you can join with this invite).

Citations

If you use nf-core/proteinfamilies for your analysis, please cite it using the following doi: 10.5281/zenodo.14881993.

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.

Owner

  • Name: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/proteinfamilies: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [MMseqs2](https://pubmed.ncbi.nlm.nih.gov/33734313/)

> Mirdita M, Steinegger M, Breitwieser F, Söding J, Levy Karin E. Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics. 2021 Sep 15;37(18):3029-31. doi: 10.1093/bioinformatics/btab184. PubMed PMID: 33734313; PubMed Central PMCID: PMC8479651.

- [FAMSA](https://pubmed.ncbi.nlm.nih.gov/27670777/)

> Deorowicz S, Debudaj-Grabysz A, Gudyś A. FAMSA: Fast and accurate multiple sequence alignment of huge protein families. Scientific reports. 2016 Sep 27;6(1):33964. doi: 10.1038/srep33964. PubMed PMID: 27670777; PubMed Central PMCID: PMC5037421.

- [mafft](https://pubmed.ncbi.nlm.nih.gov/23329690/)

> Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution. 2013 Jan 16;30(4):772-80. doi: 10.1093/molbev/mst010. PubMed PMID: 23329690; PubMed Central PMCID: PMC3603318.

- [ClipKIT](https://pubmed.ncbi.nlm.nih.gov/33264284/)

> Steenwyk JL, Buida III TJ, Li Y, Shen XX, Rokas A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLoS biology. 2020 Dec 2;18(12):e3001007. doi: 10.1371/journal.pbio.3001007. PubMed PMID: 33264284; PubMed Central PMCID: PMC7735675.

- [hmmer](https://pubmed.ncbi.nlm.nih.gov/29905871/)

> Eddy SR. Accelerated profile HMM searches. PLoS computational biology. 2011 Oct 20;7(10):e1002195. doi: 10.1371/journal.pcbi.1002195. PubMed PMID: 22039361; PubMed Central PMCID: PMC3197634.

- [HH-suite3](https://pubmed.ncbi.nlm.nih.gov/31521110/)

> Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC bioinformatics. 2019 Dec;20:1-5. doi: 110.1186/s12859-019-3019-7. PubMed PMID: 31521110; PubMed Central PMCID: PMC6744700.

- [SeqKit](https://pubmed.ncbi.nlm.nih.gov/38898985/)

> Shen W, Sipos B, Zhao L. SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. 2024 Apr 5:e191. doi: 10.1002/imt2.191. PubMed PMID: 38898985; PubMed Central PMCID: PMC11183193.

- [Biopython](https://pubmed.ncbi.nlm.nih.gov/19304878/)

> Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, De Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 6;25(11):1422. doi: 10.1093/bioinformatics/btp163. PubMed PMID: 19304878; PubMed Central PMCID: PMC2682512.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 37
  • Issues event: 25
  • Release event: 5
  • Watch event: 16
  • Delete event: 31
  • Issue comment event: 21
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  • Pull request review comment event: 126
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  • Pull request event: 104
  • Fork event: 2
Last Year
  • Create event: 37
  • Issues event: 25
  • Release event: 5
  • Watch event: 16
  • Delete event: 31
  • Issue comment event: 21
  • Push event: 187
  • Pull request review comment event: 126
  • Pull request review event: 128
  • Pull request event: 104
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 17
  • Total pull requests: 60
  • Average time to close issues: 12 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 6
  • Average comments per issue: 0.18
  • Average comments per pull request: 0.15
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 17
  • Pull requests: 60
  • Average time to close issues: 12 days
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 6
  • Average comments per issue: 0.18
  • Average comments per pull request: 0.15
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • vagkaratzas (15)
  • jen-reeve (1)
Pull Request Authors
  • vagkaratzas (49)
  • nf-core-bot (5)
  • gabryvzz (1)
  • GiatrasKon (1)
  • ChrisTzaferis (1)
  • sillitoe (1)
Top Labels
Issue Labels
enhancement (12) bug (3)
Pull Request Labels

Dependencies

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