Conservation & Molecular Ecology @Brown
  • Home
  • People
  • Publications
  • Research
  • Conservation
  • News
  • Join
  • Contact

Bioinformatics Workshop Archive

Mpala Reference Library formatted for "dada2"

6/18/2021

0 Comments

 
Collaborator Nick Harvey has kindly provided a formatted version of our current Mpala Plant DNA Barcode Reference Library that is suitable for taxonomic assignments using the R package dada2. You can download the fasta file of reference library v.2.0 (corresponding to Gill et al. 2019) formatted for dada2 here.

​Thank you, Nick, for making this time-saving resource available to share!
0 Comments

Workflows for denoising Illumina amplicon data using dada2 and Oscar

1/29/2019

0 Comments

 
Bianca Brown began the hard work of collating scripts the lab uses to process fastq data from our lab's diverse Illumina amplicon projects. These strategies, and a draft explanation of why we use different "flavors" of these approaches for different projects, are provided here. 

Modules included the tutorial include "cutadapt," "dada2," and "R," with some references to "Obitools" and Brown University's  supercomputing cluster "Oscar."

Many of the steps and principles of these workflows are identical -- we want to thoughtfully prepare our data for analysis and remove errors -- but a few of the nuts and bolts differ. Most often, these differences arise from whether or not a project included single-end sequence data (used to be common) or paired-end sequence data (now standard in the lab). There are also differences in approaches depending on whether the amplicons are typically invariable in length (e.g., 16S-V4 rRNA or COI markers), or if there is considerable length variation (e.g., trnL-P6 markers). 

For members of Brown University seeking to run parts of these modules on Oscar, Bianca has very kindly provided some blank bash scripts that can get you started here.

NB: This compilation of scripts is a work in progress. We are aware of necessary updates and improvements, and we intend to push them soon. We'll add posts describing any substantial updates in the future, and we welcome feedback.

We also wish to express our appreciation to all of the authors of the softwares that we use and cite in our work.
0 Comments

    Author

    Computational resources kindly contributed and explained by members of our community.

    Archives

    January 2023
    December 2022
    November 2022
    January 2022
    June 2021
    January 2021
    March 2019
    February 2019
    January 2019

    Categories

    All
    Dada2
    Data
    Data Management
    DNA Barcodes
    High-performance Computing
    Lab Protocols
    Metabarcoding
    Microbiome
    Oscar
    Phylogenetics
    Pipelines
    Reference Libraries
    R Tutorials
    Software

    RSS Feed


Picture
Copyright 2021 © Tyler Kartzinel

  • Home
  • People
  • Publications
  • Research
  • Conservation
  • News
  • Join
  • Contact