Webinar Resources

What can you find here?

  1. Links to our recorded webinar, available on the OSU Office of Research YouTube channel
  2. Softwares/tools relevant to each webinar topic

1. Past webinar recordings (redirects to YouTube):

  • March 2, 2021 –  view here: Introduction to microbiome science and why OSU ? | Matt Sullivan (OSU)
  • March 9, 2021 –  view here: Introduction to high-performance computing (HPC) | Shareef Dabdoub (OSU)
  • March 16, 2021 – view here: Introduction to QIIME, Mothur and ecological statistics for microbiomes | Shareef Dabdoub (OSU)
  • March 23, 2021 – view here: VirION2 – hybrid short-/long-read virus metagenomics | Olivier Zablocki (OSU)
  • March 30, 2021 – view here: Front-end metagenome processing to MAGs (QC, assemble, read map, binning) | Dylan Cronin (OSU)
  • April 6, 2021 – view here: DRAM and genome-resolved inference | Kayla Borton & Mike Shaffer (Colorado State University)
  • April 13, 2021 – view here | Genome-based taxonomy and phylogenomics | Donovan Parks (Australian Centre for Ecogenomics)
  • April 20, 2021 – view here | Viromics 1 – iVirus, KBase and IMG/VR overview of ‘virus’ tools available | Ben Bolduc (OSU)
  • April 27, 2021 – view here | Viromics 2 – the viral ecogenomic pipeline | Ben Bolduc (OSU)
  • May 4, 2021 – view here | Advanced ecological statistics for microbiomes | Ahmed Zayed (OSU)

2. Software/tools for each webinar session:

March 16, 2021 | Introduction to QIIME, Mothur and ecological statistics for microbiome:

  • Github repo for this webinar: https://github.com/smdabdoub/MicrobiomeInformaticsWebinarWeek3
  • R libraries: dada2, phyloseq, biomformat, here, tidyverse (or just: stringr, readr, tibble, ggplot2), tictoc, mixOmics, randomForest, caret, magrittr (part of tidyverse)
  • QIIME2: install instructions: https://docs.qiime2.org/2019.10/install/
  • Mothur:
    • pre-built binaries: https://mothur.org/wiki/installation/.
    • Install with conda: conda create -n mothur-1.44.1 -c conda-forge -c bioconda mothur==1.44.1
  • Test data:
    • 16S data: https://www.dropbox.com/s/vuwmc95jel15dxn/mouse-gut-data.zip?dl=0
    • Mothur reference data: https://www.dropbox.com/s/k28xjy27fpxp1lh/mothur-ref.zip?dl=0
    • dada2 taxonomy data: https://www.dropbox.com/s/bals51okrhcszsh/dada2-tax-training.zip?dl=0

March 23, 2021 |VirION2 – hybrid short-/long-read virus metagenomics | Olivier Zablocki (OSU)

 

April 6, 2021 | DRAM and genome-resolved inference | Kayla Borton & Mike Shaffer (Colorado State University)

All the materials related to DRAM webinar can be accessed here: https://www.dropbox.com/sh/newkcnc4yhrbrrc/AADVP7Y-h6FYRO5IM7Opz3a1a?dl=0

 

April 13, 2021 | Genome-based taxonomy and phylogenomics | Donovan Parks (Australian Centre for Ecogenomics)

  • Background reading and literature cited during the webinar:
    • Genomics and the bacterial species problem Link
    • Polyphasic taxonomy, a consensus approach to bacterial systematics Link
    • A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Link
    • A complete domain-to-species taxonomy for Bacteria and Archaea Link
    • Genome sequences as the type material for taxonomic descriptions of prokaryotes Link
    • Roadmap for naming uncultivated Archaea and Bacteria Link
    • International Code of Nomenclature of Prokaryotes Link
  • Nomenclatural resources:
    • LPSN: List of Prokaryotic names with Standing in Nomenclature Link
    • Bergey’s Manual of Systematic of Archaea and Bacteria Link
    • NamesForLife Link
  • Taxonomic resources:
    • GTDB: Genome Taxonomy Database Link
    • NCBI Taxonomy Link
    • SILVA: high-quality ribosomal RNA databases Link
  • Bioinformatic tools:
    • GTDB-Tk: Genome Taxonomy Database Toolkit, delineates species using ANI and higher rank using RED Link
    • MiGA: Microbial Genome Atlas, delineates taxa using AAI and ANI Link
    • TYGS: Type Strain Genome Server, delineates taxa using Genome BLAST Distance Phylogeny Link
    • FastANI Link

April 20/April 27, 2021 | Viromics – the viral ecogenomic pipeline | Ben Bolduc (OSU)

May 4, 2021 | Advanced ecological statistics for microbiomes | Ahmed Zayed (OSU)

  • Materials needed for this webinar can be found here.