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bigbacter-nf

Bacterial surveillance pipeline.

https://github.com/doh-jdj0303/bigbacter-nf

Science Score: 44.0%

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary

Keywords

accessory-genome bacterial-genomics clustering-analysis genome-analysis public-health public-health-surveillance snp-analysis
Last synced: 9 months ago · JSON representation ·

Repository

Bacterial surveillance pipeline.

Basic Info
  • Host: GitHub
  • Owner: DOH-JDJ0303
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Homepage:
  • Size: 6.7 MB
Statistics
  • Stars: 24
  • Watchers: 1
  • Forks: 4
  • Open Issues: 4
  • Releases: 3
Topics
accessory-genome bacterial-genomics clustering-analysis genome-analysis public-health public-health-surveillance snp-analysis
Created almost 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

BigBacter

Overview

BigBacter is a pipeline aimed at simplifying bacterial genomic surveillance.

Main features 1) Saves your samples to a personal database (can be stored locally or on the cloud) 2) Includes database samples when they are closely related to new samples 3) Optimized to reduce core genome shrinkage 4) Optimized for speed and resource usage 5) Multiple species/subtypes can be included in a single run 6) Generates report-ready figures

Main analyses: 1) Recombination-aware core SNP analysis (Snippy and Gubbins) 2) Accessory distance analysis (PopPUNK) 3) Phylogenetic analysis (IQTREE2 or Rapidnj)

Main outputs: 1) Phylogenetic trees (Core SNPs) 2) Distance matrices (Accessory distance and Core SNPs) 3) Tabulated summary (QC metrics, linkage summaries, and more!) 4) Outputs are summarized in Microreact files 🙌

Required Inputs |Column Name|Description| |-|-| |sample|sample name| |taxa|sample taxonomy (species or lower)| |assembly|assembly file| |fastq1|foward read| |fastq2|reverse read|

BigBacter also requires a taxon-specific PopPUNK database (pre-made databases can be found here). (https://www.bacpop.org/poppunk/))

[!TIP] BigBacter is designed to run after general bacterial analysis (e.g, PHoeNIx, Bactopia, TheiaProk.)

How to use BigBacter:

1) Quick Start 2) Full Instructions

Checkout the wiki to learn more!

BigBacter was originally created by Jared Johnson for the Washington State Department of Health. See a full list of contributors here.

Owner

  • Login: DOH-JDJ0303
  • Kind: user

Citation (CITATIONS.md) 

# nf-core/bigbacter: 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/)

- [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)

- [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: 9
  • Issues event: 16
  • Release event: 1
  • Watch event: 7
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 8
  • Push event: 20
  • Pull request event: 12
  • Fork event: 1
Last Year
  • Create event: 9
  • Issues event: 16
  • Release event: 1
  • Watch event: 7
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 8
  • Push event: 20
  • Pull request event: 12
  • Fork event: 1

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v1 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v1 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi