In order for this training to be effective for all students participating, each student should perform the following before the first class:
- Confirm that they can connect to their VM.
- Watch a 75 minute video on the linux operating system.
- Watch a short video on tmux, a linux application that allows for multiple terminals.
Connect to your VM
In the slack channel will be listed your VM IP address, along with a ssh key file. This information will be posted on Monday, June 29th. In order to connect to this VM, you will need to download the terminal program MobaXterm. MobaXterm can be downloaded from https://mobaxterm.mobatek.net/download-home-edition.html. IMPORTANT: Please download the “Portable edition”, not the “Installer edition”. The “Portable edition” will allow you to run the application without installing it, thus no admin rights needed. Once you have downloaded MobaXterm and have access to your IP address and ssh key, watch the youtube video on How to Connect to Your VM. I will also post the username and passphrase in slack.
The video link is https://www.youtube.com/watch?v=oxuRxtrO2Ag. This video will give you a basic understanding of navigating around the bash terminal in linux. It is well worth the 75 minutes before the course, working within your own VM.
Many of the processes we will be running will require long processing times that could be interrupted by network connection issues. To avoid this, we will perform the exercises in the class using the tmux application. This tmux tutorial video will guide you through the process of using tmux.
Some additional resources that you will find useful when starting out are:
Session 1 - Linux - Monday July 6th, 12 PM and 2 PM MDT
Session 2 - Background on Viral Genomics and Coronaviruses - Tuesday, July 7th, 12 PM and 2 PM MDT
Session 3 - Sequencing Methods for SARS-CoV-2 - Wednesday July 8th, 12 PM and 2 PM MDT
Session 4 - StaPH-B Toolkit - Monday July 13th, 12 PM and 2 PM MDT
Session 5 - UPHL BioNGS - Tuesday July 14th, 12 PM and 2 PM MDT
Session 6 - Commercial Options - Wednesday July 15th, 12 PM and 2 PM MDT
Session 7 - NGS Data Visualization for QC of Results - Monday July 20th, 12 PM and 2 PM MDT
Session 8 - Data Sharing with GISAID and NCBI - Tuesday July 21st, 12 PM and 2 PM MDT
Session 9 - Data Visualization in Nextstrain - Wednesday July 22nd, 12 PM and 2 PM MDT
Office hours will be offered each week on Thursday from 2 PM to 4 PM MDT, on Friday from 9 AM to 11 AM MDT, and by request.
Expanded Agenda (will contain links, videos, code, as course progresses)
Session 1 - Linux
- Linux basics
- Working in Tmux
- Connecting to Basespace
- Connecting to cloud resources
- Transferring data to your VM for the class
Commands used in this session
***bash commands*** dir #lists out a directory ls #also lists out a directory ls -la #lists out a directroy with details ll #alias for ls -la cd <directory> #change directory cd #will bring you to your home directory mkdir <dir> #make directory rmdir <dir> #remove directory if it is empty rm -rf <dir> #remove directory if it is full gzip <name.fastq> #zip a read file ***tmux*** tmux ls #list open tmux sessions tmux new -s <name> #start a tmux session called <name> tmux a -t <name> #attach to tmux session called <name> tmux kill-session -t <name> #kill tmux session called <name> Ctrl-b , #rename current window Ctrl-b c #create new window Ctrl-b n #go to next window tmux info #help ***basespace cli*** bs auth #authenticate to Basespace bs list projects #list projects in basespace bs download project -n <name> -o <dir> #download project files to <dir> ***gsutils*** gsutil ls #list storage buckets gsutil cp <source> <destination> #cp data from storage bucket ***sra-toolkit*** - might need to "sudo apt-get install sra-toolkit" prefetch <sra_id> fastq-dump --split-files --gzip <sra_id>
Session 2 - Background on Viral Genomics and Coronaviruses
- Viral genomics primer
- Considerations of bacteria vs viral pathogens
- Coronavirus, the new flu.
- Papers on Coronaviruses
REMINDER 7/7 –> register for a GISAID account
Session 3 - Sequencing Methods for SARS-CoV-2
Session 4 - StaPH-B Toolkit
Recording for Session 4 - 12 PM MDT (Watch the 3 PM instead)
Recording for Session 4 - 3 PM MDT (This is the better recording)
- Monroe pipeline
Some commands to make today’s session easier
tmux new -s session4 mkdir session4-1 cd session4-1 gsutil ls gsutil ls gs://mtn-reads/ gsutil -m cp -r gs://mtn-reads/session4/* . tar -xf reads.tar mkdir reads mv *.gz reads rm reads.tar staphb-wf monroe staphb-wf monroe pe_assembly staphb-wf monroe pe_assembly --primers V3 --output pe_assembly_1 --config 20-07-11_pe_assembly.config reads staphb-wf monroe cluster_analysis staphb-wf monroe cluster_analysis --output cluster_analysis_1 --config 20-07-11_cluster_analysis.config pe_assembly_1/assemblies/
Session 5 - UPHL BioNGS
Some commands to make today’s exercises easier
#see if you have a tmux session open tmux ls #create a new tmux session called session5 tmux new -s session5 #create new window in your tmux session <create new window in tmux with Ctrl-b, c> #copy over session files gsutil -m cp -r gs://mtn-reads/session5/* . #extract the session files tar -xf session5_files_2.tar #change dir into cecret_session5 cd cecret_session5 #check out covid_samples.txt column -t covid_samples.txt | less -S #copy new Cecret.nf to your Cecret folder cp Cecret.nf ~/Cecret/ #check thatt Cecret.nf was updated ll ~/Cecret #launch Cecret - will take about 50 minutes with 10 specimens ~/nextflow run ~/Cecret/Cecret.nf -c cecret.docker.nextflow.google.config #go up one directory to session5 cd .. #unpack bakeshow data tar -xf session5_files.tar #move into bakeshow directory cd cecret_bakeshow #check out run_results.txt column -t run_results.txt | less -S
Session 6 - Cecret and Monroe Continued
UPDATE: Most likely we will continue looking at Monroe and Cecret results
Session 7 - Data Sharing with GISAID and NCBI
- Data sharing with GISAID
Topics not covered, future webinars:
Session 8 - Data Sharing with GISAID and NCBI
- Data sharing with SRA
Session 9 - More Data Sharing
- Data sharing with Genbank
Topics not covered below, will have future webinars.