Bioinformatics Workshop

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Short Course and WORKSHOP AT 2017 Conference of research workers in animal diseases (CRWAD):



Development of this course was supported by USDA-NIFA Grant Number 2015-68003-23048



Workshop Description:

The Microbial Ecology Group at Colorado State University is pleased to announce an upcoming Short Course and Workshop: “Bioinformatics and Statistics for Shotgun Metagenomic Research.”  This event is designed to provide participants with the basic background and tools needed to analyze the microbiome and resistome data obtained from shotgun metagenomic sequencing.  This event is being held in conjunction with the 98th Annual Conference of Research Workers in Animal Diseases (CRWAD) and is Co-Sponsored by the Association for Veterinary Epidemiology and Preventive Medicine (AVEPM).

Day 1: Bioinformatics with the AMR++ Nextflow Pipeline

December 2nd, 2017; 9am-5pm — The first day of the short course will be aimed at understanding the bioinformatics behind metagenomic high-throughput sequencing data processing.  Attendees will gain a working knowledge of the methods behind the AMR++ Nextflow metagenomic analysis pipeline, become familiar with the basics of navigation on the GNU/Linux command line, be introduced to the Amazon Web Services for bioinformatics processing, and obtain hands-on experience with running the AMR++ Nextflow pipeline on a data set derived from real metagenomic sequencing data.  Day 1 will conclude with the production of the count matrix, which is the input for statistical analysis of metagenomic data, to be discussed on Day 2 of the short course.

Day 1 Topics

(Lecture) Overview of high-throughput sequencing (HTS)

Image credit: ssilver / 123RF Stock Photo

(Lecture) Skillsets and teams needed for conducting research using HTS

(Lecture) Practical considerations for using HTS in research

(Lecture) Dealing with host contamination in HTS sequencing

(Lecture) Assessing sequencer output (FASTQ data)

(Lecture) Overview of AMR++ bioinformatics workflow (Lakin et al., Nucleic Acid Research, 2017)

  • Sequence quality control, filtering, and trimming: how it’s done and why to do it
  • Alignment algorithms: pros, cons, and AMR++ approach
  • k-mer algorithms for microbiome classification: pros, cons, and AMR++ approach
  • Antimicrobial resistance and HTS microbiome database resources
  • Assessing rarefaction with AMR++

 (Lecture) Cloud computing options with Amazon Web Services (AWS)

 (Workshop) Connecting to an AWS instance

(Workshop) Navigating the GNU/Linux command line

(Workshop) Manipulating directories

(Workshop) Working with files, permissions, and executables in GNU/Linux shell

(Workshop) Transfering files to the AWS cloud with File Transfer Protocol (FTP)

(Workshop) Run AMR++ with Example Data

(Workshop) Troubleshooting AMR++ errors and interruptions

(Workshop) Analyzing pipeline output

(Workshop) Creating metadata files for subsequent statistical analysis

Day 2: Statistical Analysis of Microbiome/Metagenomic Count Data with the AMR++ Shiny App

December 3rd, 2017; 9am-12pm — Day 2 of the short course will be aimed at understanding how to proceed from bioinformatics processing of data through statistical analysis of the count matrix.  Often, bioinformatics pipelines do not include enough statistical options to allow the researcher to obtain an answer to the research question being asked, and no clear direction is given for how to proceed with statistical analysis.  In this workshop, attendees will gain an understanding of the methods behind modern statistical analysis of metagenomic and microbiome count data using a newly developed, graphical interface through the AMR++ Shiny App.  The focus of these lectures will be on applying statistical methods in a hands-on way and interpreting the results of regression modeling for differential abundance analysis.

Day 2 Topics

(Lecture) Understanding the count matrix for statistical analysis

(Lecture) Exploratory analysis of count data

(Lecture) Normalization vs. rarefaction for biological count data

(Lecture) Intro to regression techniques for differential abundance

(Workshop) Installing/Updating the AMR++ Shiny App

(Workshop) Loading count data into the AMR++ Shiny App

(Workshop) Exploratory graphing with the AMR++ Shiny App

(Workshop) Regression and interpretation of statistical results with the AMR++ Shiny App 


Workshop activities will be held at the Chicago Marriott, Downtown Magnificent Mile, in Chicago, Illinois, which is the Conference Headquarters for the 98th Annual Conference of Research Workers in Animal Diseases (CRWAD).


Workshop Day 1 – December 2nd, 2017: 9AM-5PM

Workshop Day 2 – December 3rd, 2017: 9AM-12PM

AVEPM Calvin Schwabe Symposium – December 3rd, 12:30-5:00PM

CRWAD 2017 Annual Meeting – December 3rd-5th                

Presented by:

Organizers and Instructors: Dr. Zaid Abdo, Dr. Keith Belk, Chris Dean, Enrique Doster, Steven Lakin, Dr. Paul MorleyDr. Noelle Noyesand  Maggie Weinroth

College of Veterinary Medicine & Biomedical Sciences and College of Agricultural Sciences, Colorado State University


Meeting Registration for the one-and-a-half-day program is $400*.  Pre-registration is REQUIRED.  Please use this link to make a secure online payment, and to reserve your spot in this course.

Course Preparation:

In order to get the most of this course, we strongly encourage participants to prepare by gaining familiarity with use of command line coding for basic server navigation and manipulation of files.  We recommend using the free online tutorial available from ( for this purpose.  Obtain a free account at this site, navigate to CATALOG in the upper right corner of the home page, then click on LEARN THE COMMAND LINE module.


Using one-on-one interactive learning is a key method for this course. As such, all participants should bring a laptop computer with the following minimum system requirements:

Minimum operating system:

  • Windows Vista or higher -or-
  • Mac OS X 10.6+  -or-
  • Ubuntu 12.04-15.10/Debian 8  -or-
  • Fedora 19+/RedHat 7+/openSUSE 13.1+   

WiFi Capability

Required Software: Updated versions of R and RStudio:

Additional Details:

There are several ongoing airline seat sales that we have noticed, which cover these dates, so you may want to buy early and save!

 You can make room reservations at the Chicago Marriott, Downtown Magnificent Mile, in Chicago, by following this link (Chicago Marriott Downtown Room Reservations)

Information regarding Featured Keynote Speakers for the 2017 CRWAD Conference, registrations and other meeting details, and information for submitting abstracts for the CRWAD meeting can be found at  

Deadline for abstract submission is Aug 31, 2017.

Deadline for early-bird CRWAD registration is Nov 17, 2017.

We encourage you to subscribe to the listserv dedicated to this workshop to ensure that you receive important notifications: 

 You can also contact Dr. Paul Morley for additional course details (

*Registration and Cancellation Information:  Pre-registration is required for this course. Courses are subject to cancellation when registration is inadequate to cover costs of the program. Registration at least four weeks before the course will help prevent cancellation. Course fee is payable to Colorado State University. Fee includes proceedings, materials, and supplies.