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demultiplextagseq

Demultiplex 3-tag rna-seq data

https://github.com/ax-ekk/demultiplextagseq

Science Score: 57.0%

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Repository

Demultiplex 3-tag rna-seq data

Basic Info
  • Host: GitHub
  • Owner: ax-ekk
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 72.3 KB
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Created 12 months ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Citation

README.md

demultiplextagseq

Introduction

demultiplextagseq is a bioinformatics pipeline to demultiplex 3'-tag-seq data. It performs the following steps:

  1. Read QC (FastQC) multiplexed sample (paired-end)
  2. Extract barcodes (UMI-tools extract)
  3. Demultiplex samples (fqtk)
  4. Read QC (FastQC) demultiplex samples (single-end)
  5. Plot selected quality metrics across 96-well plate
  6. Combine and visualize (MultiQC)

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,fastq_1,fastq_2 SAMPLEID1_PAIRED_END,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz SAMPLEID2_PAIRED_END,HEG587A1_S1_L002_R1_001.fastq.gz,HEG587A1_S1_L002_R2_001.fastq.gz

Each row represents a pair of fastq files (paired end). This should come from the 3'tag-seq protocol. In many cases there will be only one row, but if several plates have been prepared, they can be demultiplexed in parallel.

Now, you can run the pipeline using:

bash nextflow run berger demultiplextagseq \ -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.

Parameters

The pipeline takes the following optional pipeline specific paramters:

| Parameter | Description | | ------------- | ---------------------------------------------------------------------------------------------------------------------------- | | --splitfastq | Should the multiplexed input fastq file(s) be split
into smaller chuncks to speed up pipleline?
(Default: true) | | --splitsize | Size of the fastq chunks.
(Default 50.000.000) |

In addition, nextflow specific parameters can be used, such as: -resume, -w etc. See Nextflow Docs for more details.

Output

The pipeline outputs a folder named after the -outdir parameter. This folder contain the following subfolders:

  • fastqc: fastqc report for multiplexed and demultiplexed samples
  • fqtk: demultiplexed fastq files to be used for analysis named by well
  • multiqc: multiqc report summarizing QC and methods
  • pipeline_info: info about the pipeline run
  • umitools: umitool logs

Credits

demultiplextagseq was written by Elin Axelsson-Ekker, strongly inspired by Yoav Voicheck's original python script

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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

  • Login: ax-ekk
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Citation (CITATIONS.md) 

# demultiplextagseq: 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

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

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [UMI-tools](https://genome.cshlp.org/content/27/3/491)

> Smith, T., Heger, A., & Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome research, 27(3), 491–499. doi:10.1101/gr.209601.116. PMID: 28100584

- [fqtk](https://github.com/fulcrumgenomics/fqtk)


- [R](https://www.R-project.org/)

> R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

- [tidyverse](https://www.tidyverse.org/1)

> Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T., Miller, E., Bache, S., Müller, K., Ooms, J., Robinson, D., Seidel, D., Spinu, V., … Yutani, H. (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686. doi:"10.21105/joss.01686"

- [fastqcr](https://rpkgs.datanovia.com/fastqcr/index.html)

> Kassambara A (2023). fastqcr: Quality Control of Sequencing Data. R package version 0.1.3,

- [cowplot](https://github.com/wilkelab/cowplot)

> Wilke C (2025). cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'. R package version 1.1.3.9000,.

- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)

> Neuwirth E (2022).  *RColorBrewer: ColorBrewer Palettes* . R package version 1.1-3

- [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.
  >

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Dependencies

modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/fqtk/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/umitools/extract/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfschema_plugin/meta.yml cpan
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/fqtk/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/umitools/extract/environment.yml pypi