Data

Tools

Indexes

Applications

Experiments

Open Source Science

getprimers

Pipeline for primer design in batches

https://github.com/barbarahelena/getprimers

Science Score: 54.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Pipeline for primer design in batches

Basic Info
  • Host: GitHub
  • Owner: barbarahelena
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage:
  • Size: 1.39 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 11 months ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

getprimers

Nextflow run with conda run with docker run with singularity

Introduction

getprimers is a bioinformatics pipeline that generates primers and checks the quality and specificity.

  1. Design primers using Primer3
  2. Check quality of primers using Primer3
  3. Optional: pull reference genomes if working with bacterial proteins, using NCBI-genome-download
  4. Check specificity of primers using BLAST against reference genomes
  5. Process results: select primers that were not flagged and merge one primer set per protein into one output table.

getprimersworkflow

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_bacteria.csv:

```csv protein_ID,taxonomy,sequence

``` Each row represents a protein.

Now, you can run the pipeline using:

bash nextflow run getprimers \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --genome hg38 \ --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 documentation. There is also a more specific output doc.

Credits

getprimers was written by me, but I tried to follow the nf-core template as much as possible.

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.

Owner

  • Name: Barbara Verhaar
  • Login: barbarahelena
  • Kind: user
  • Location: Amsterdam

PhD candidate @ Amsterdam UMC Vascular medicine

Citation (CITATIONS.md) 

# nf-core/getprimers: 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].

- [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
  • Push event: 5
  • Pull request event: 2
  • Create event: 4
Last Year
  • Push event: 5
  • Pull request event: 2
  • Create event: 4

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v4 composite
  • octokit/request-action v2.x composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v4 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
.github/workflows/ci.yml actions
  • actions/checkout 11bd71901bbe5b1630ceea73d27597364c9af683 composite
  • conda-incubator/setup-miniconda a4260408e20b96e80095f42ff7f1a15b27dd94ca composite
  • eWaterCycle/setup-apptainer main composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0b93645e9fea7318ecaed2b359559ac225c90a2b composite
  • eWaterCycle/setup-apptainer 4bb22c52d4f63406c49e94c804632975787312b3 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout 11bd71901bbe5b1630ceea73d27597364c9af683 composite
  • actions/setup-python 0b93645e9fea7318ecaed2b359559ac225c90a2b composite
  • peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
.github/workflows/linting.yml actions
  • actions/checkout 11bd71901bbe5b1630ceea73d27597364c9af683 composite
  • actions/setup-python 0b93645e9fea7318ecaed2b359559ac225c90a2b composite
  • actions/upload-artifact b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 composite
  • nf-core/setup-nextflow v2 composite
  • pietrobolcato/action-read-yaml 1.1.0 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact 80620a5d27ce0ae443b965134db88467fc607b43 composite
  • marocchino/sticky-pull-request-comment 331f8f5b4215f0445d3c07b4967662a32a2d3e31 composite
.github/workflows/release-announcements.yml actions
  • actions/setup-python 0b93645e9fea7318ecaed2b359559ac225c90a2b composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action 80dbe0a7697de18c15ad22f4619919ceb5ccf597 composite
.github/workflows/template_version_comment.yml actions
  • actions/checkout 11bd71901bbe5b1630ceea73d27597364c9af683 composite
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
  • nichmor/minimal-read-yaml v0.0.2 composite
modules/nf-core/bowtie2/build/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/bowtie2/build/environment.yml pypi