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dadaist2

Dadaist2 🟨 Highway to R

https://github.com/quadram-institute-bioscience/dadaist2

Science Score: 65.0%

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    Low similarity (9.8%) to scientific vocabulary

Keywords

16s amplicon-pipeline asv bioinformatics dada2 metabarcoding phyloseq taxonomy
Last synced: 4 months ago · JSON representation ·

Repository

Dadaist2 🟨 Highway to R

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 5
  • Open Issues: 2
  • Releases: 17
Topics
16s amplicon-pipeline asv bioinformatics dada2 metabarcoding phyloseq taxonomy
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

dadaist2

Dadaist2 logo

release version Conda Dadaist-CI

Standalone wrapper for DADA2 package, to quickly generate a feature table and a set of representative sequences from a folder with Paired End Illumina reads.

Dadaist2 stable

Please check the legacy documentation and tutorials for installation and usage notes.

Dadaist2 2.x under development

Please check the online documentation for dev

Cite

Ansorge, R., Birolo, G., James, S. A., & Telatin, A. (2021). Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments. International journal of molecular sciences, 22(10), 5309. 10.3390/ijms22105309

Owner

  • Name: Quadram Institute Bioscience
  • Login: quadram-institute-bioscience
  • Kind: organization

Citation (CITATION.cff) 

# YAML 1.2
---
authors: 
  -
    family-names: Telatin
    given-names: Andrea
    affiliation: Quadram Institute Bioscience, UK
  -
    family-names: Rebecca
    given-names: Ansorge
    affiliation: Quadram Institute Bioscience, UK
  -
    family-names: Giovanni
    given-names: Birolo
    affiliation: University of Turin, IT
  -
    family-names: Steve
    given-names: James
    affiliation: Quadram Institute Bioscience, UK
cff-version: "1.1.0"
doi: "10.3390/ijms22105309"
identifiers: 
  - 
    type: url
    value: "https://quadram-institute-bioscience.github.io/dadaist2/"
license: MIT
message: "If you use this software, please cite it using these metadata."
title: "Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments"
abstract: "The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as ‘Amplicon Sequence Variants’ (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic."
...

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 5
  • Push event: 4
Last Year
  • Issues event: 2
  • Issue comment event: 5
  • Push event: 4

Issues and Pull Requests

Last synced: 4 months ago

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  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 3 months
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  • Total pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
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  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 1
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Top Authors
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  • najibveto (2)
  • jzrapp (1)
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Dependencies

lab/class/environment.yml conda
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