LINKS & FILES FOR PATRIC, SEED, PHAGE RAST, AND RESISTOME TUTORIALS

*NEW* 2019-2020 RESISTOME TUTORIALS

Find the data you will need here

• University of Buenos Aires Bioinformatics Course (September 2020)
  • Link to PATRIC https://patricbrc.org
  • You can find freshly assigned metagenomes here: skin / gut
  • Previously analyzed example (skin)
     
  • Advanced: Do-it-yourself on a Linux terminal: workflow/synopsis

• GE-GPX Workshop (December 11, 2019) assigned metagenomes: skin / gut
  • Link for the R activities: http://35.227.174.188/
  • You can find the data for the R activity here: https://drive.google.com/drive/folders/197y6DidHvc5Ze_ZPDxCJH6tovfo1ILs7
    • Or if you want, download the entire synopsis here as a PDF: workshop-datavis-intro.pdf and workshop-rnaseq.pdf 

Some useful tips:

• Linux primer: Common Linux commands
• FASTA files

LINKS

• Online RAST (classic & tk)
• Download latest RASTtk (standalone version): allows batch annotations
• PhAnToMe Gene Caller (previously PhAST): alternative gene calling that can be directly submitted to RAST
• IRIS (command-line environment)
• How to use RASTtk for batch annotation (uploading multiple genomes)

TEST READS FILES

Acinetobacter baumannii sequence reads

• bau_sim_R1.fq (~58 MB)
• bau_sim_R2.fq (~58 MB)

TEST PHAGE FILES

• T4
• T7
• Lambda

PRESENTATIONS

• Part 1:
  • PDF file: Part1.pdf
  • Link to Slide Share: bit.ly/annotation2016
• Part 2:
  • PDF file: Part2.pdf
  • Link to Slide Share: bit.ly/phantome4
• 2017 presentations:
  • Evergreen 2017 Phage Workshop Intro: Link bit.ly/phigenomics2017
  • Evergreen 2017 Phage Annotation Workshop (by RKA): Link bit.ly/phantome2017
  • Evergreen 2017 Phage Metagenomics Workshop (by Alejandro Reyes):PDF file
• VoM 2018 presentations:
  • Intro: http://bit.ly/annotation2018 (PDF)
  • RAST and RASTtk: http://bit.ly/phageRAST2018 (PDF)
  • PATRIC: http://bit.ly/phagePATRIC (PDF)