dualrnaseq

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

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

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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1 of 6 committers (16.7%) from academic institutions
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Scientific vocabulary similarity
Low similarity (12.7%) to scientific vocabulary

Keywords

dualrna-seq host-pathogen nextflow nf-core pipeline quantification readmapping rna-seq workflow

Last synced: 6 months ago · JSON representation ·

Repository

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Basic Info

Host: GitHub
Owner: nf-core
License: mit
Language: Nextflow
Default Branch: master
Homepage: https://nf-co.re/dualrnaseq
Size: 45 MB

Statistics

Stars: 22
Watchers: 133
Forks: 36
Open Issues: 46
Releases: 1

Topics

dualrna-seq host-pathogen nextflow nf-core pipeline quantification readmapping rna-seq workflow

Created over 5 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

Dual RNA-seq pipeline

nf-core/dualrnaseq is a bioinformatics pipeline built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Introduction

nf-core/dualrnaseq is specifically used for the analysis of Dual RNA-seq data, interrogating host-pathogen interactions through simultaneous RNA-seq.

This pipeline has been initially tested with eukaryotic host's including Human and Mouse, and pathogens including Salmonella enterica, Orientia tsutsugamushi, Streptococcus penumoniae, Escherichia coli and Mycobacterium leprae. The workflow should work with any eukaryotic and bacterial organisms with an available reference genome and annotation.

Method

The workflow merges host and pathogen genome annotations taking into account differences in annotation conventions, then processes raw data from FastQ inputs (FastQC, BBDuk), quantifies gene expression (STAR and HTSeq; STAR, Salmon and tximport; or Salmon in quasimapping mode and tximport), and summarises the results (MultiQC), as well as generating a number of custom summary plots and separate results tables for the pathogen and host. See the output documentation for more details.

Workflow

The workflow diagram below gives a simplified visual overview of how dualrnaseq has been designed.

nf-core/dualrnaseq

Documentation

The nf-core/dualrnaseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

Credits

nf-core/dualrnaseq was coded and written by Bozena Mika-Gospodorz and Regan Hayward.

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

Citations

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. ReadCube: Full Access Link

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

Owner

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

Website: http://nf-co.re
Twitter: nf_core
Repositories: 84
Profile: https://github.com/nf-core

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

Citation (CITATIONS.md)

# nf-core/dualrnaseq: 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

* [BBTools](https://jgi.doe.gov/data-and-tools/bbtools/)

* [Cutadapt](https://doi.org/10.14806/ej.17.1.200)
  > Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12

* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

* [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)
  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.

* [HTSeq](https://pubmed.ncbi.nlm.nih.gov/25260700/)
  > Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638. Epub 2014 Sep 25. PMID: 25260700; PMCID: PMC4287950.

* [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.

* [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)
  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.

* [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)
  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

## R packages

* [R](https://www.R-project.org/)
  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

* [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

* [rtracklayer](https://pubmed.ncbi.nlm.nih.gov/19468054/)
  > Lawrence M, Gentleman R, Carey V (2009). “rtracklayer: an R package for interfacing with genome browsers.” Bioinformatics, 25, 1841-1842.

* [Tximport](https://f1000research.com/articles/4-1521/v2)
  > Soneson C, Love MI and Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences [version 2; peer review: 2 approved]. F1000Research 2016, 4:1521

## Python packages

* [Python](http://www.python.org)
  > van Rossum, G. Python tutorial, Technical Report CS-R9526, Centrum voor Wiskunde en Informatica (CWI), Amsterdam, May 1995.

* [Biopython](https://academic.oup.com/bioinformatics/article/25/11/1422/330687)
  > Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon, Biopython: freely available Python tools for computational molecular biology and bioinformatics, Bioinformatics, Volume 25, Issue 11, 1 June 2009, Pages 1422–1423

* [pysam](https://github.com/pysam-developers/pysam)

* [matplotlib](https://matplotlib.org/3.1.0/citing.html)
  > J. D. Hunter, "Matplotlib: A 2D Graphics Environment", Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, 2007

* [seaborn](http://seaborn.pydata.org/index.html)
  > Waskom, M. et al., 2017. mwaskom/seaborn: v0.8.1

## 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)

* [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: 7
Issues event: 23
Watch event: 4
Delete event: 21
Member event: 2
Issue comment event: 19
Push event: 47
Pull request review comment event: 20
Pull request review event: 31
Pull request event: 27
Fork event: 3

Last Year

Create event: 7
Issues event: 23
Watch event: 4
Delete event: 21
Member event: 2
Issue comment event: 19
Push event: 47
Pull request review comment event: 20
Pull request review event: 31
Pull request event: 27
Fork event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 489
Total Committers: 6
Avg Commits per committer: 81.5
Development Distribution Score (DDS): 0.603

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
reganhayward	r**d@g**m	194
bozmik	b**1@g**m	151
Bozena Mika-Gospodorz	b**z@h**e	137
Lars Barquist	l**t@g**m	4
nf-core-bot	c**e@n**e	2
Alexander Peltzer	a**r@u**m	1

Committer Domains (Top 20 + Academic)

nf-co.re: 1 helmholtz-hiri.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 52
Total pull requests: 78
Average time to close issues: 3 months
Average time to close pull requests: 18 days
Total issue authors: 19
Total pull request authors: 16
Average comments per issue: 0.42
Average comments per pull request: 0.79
Merged pull requests: 45
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 22
Pull requests: 15
Average time to close issues: N/A
Average time to close pull requests: 8 days
Issue authors: 3
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.33
Merged pull requests: 10
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

jen-reeve (20)
opetryk (4)
bozmik (4)
pkoscielnybio (3)
blazejszczerba (3)
ewels (2)
DorotaPikulArdigen (2)
gprezza (2)
mauro-saporita (2)
MichalStachowiakArdigen (1)
mohammedkhalfan (1)
lmReef (1)
Reef-NetValue (1)
FriederikeHanssen (1)
apeltzer (1)

Pull Request Authors

nf-core-bot (31)
bozmik (13)
regan-NV (8)
mauro-saporita (6)
ewels (5)
opetryk (4)
lmReef (4)
blazejszczerba (4)
reganhayward (2)
maxulysse (2)
KevinMenden (2)
pawelciurkaardigen (1)
MichalStachowiakArdigen (1)
rafalcode (1)
FriederikeHanssen (1)

Top Labels

Issue Labels

enhancement (27) bug (6)

Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions

conda-incubator/setup-miniconda v2 composite

.github/workflows/awstest.yml actions

conda-incubator/setup-miniconda v2 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite
technote-space/get-diff-action v4 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
actions/checkout v1 composite
actions/setup-node v1 composite
actions/setup-python v1 composite
actions/upload-artifact v2 composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

.github/workflows/push_dockerhub_dev.yml actions

actions/checkout v2 composite

.github/workflows/push_dockerhub_release.yml actions

actions/checkout v2 composite

Dockerfile docker

nfcore/base 1.12.1 build

environment.yml pypi

dualrnaseq

Science Score: 77.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Dual RNA-seq pipeline

Introduction

Method

Workflow

Documentation

Credits

Contributions and Support

Citations

Owner

Citation (CITATIONS.md)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies