This branch refers to our article:

• Robbiani DF, Gaebler C, Muecksch F, et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature. 2020;584(7821):437-442. doi:10.1038/s41586-020-2456-9

Use the branch igpipeline2_timepoint_v2 if you are interested in the analyzes of the following articles:

• Wang Z, Lorenzi JCC, Muecksch F, et al. Enhanced SARS-CoV-2 neutralization by dimeric IgA. Sci Transl Med. 2021;13(577):eabf1555. doi:10.1126/scitranslmed.abf1555

• Gaebler C, Wang Z, Lorenzi JCC, et al. Evolution of antibody immunity to SARS-CoV-2. Nature. 2021;10.1038/s41586-021-03207-w. doi:10.1038/s41586-021-03207-w

• Cho, A., Muecksch, F., Schaefer-Babajew, D. et al. Anti-SARS-CoV-2 receptor-binding domain antibody evolution after mRNA vaccination. Nature (2021). https://doi.org/10.1038/s41586-021-04060-7

• Docker Installation
• Docker Execution

On the official Docker website, click on the button "Download for Mac" for macOS users or "Download for Windows" for Windows OS users.

Regardless the selected OS, a new web page will be open and the dmg file can be downloaded clicking on the button "Get Docker"

The same web page describes:

Double-click Docker.dmg to start the install process.

When the installation completes and Docker starts, the whale in the top status bar shows that Docker is running, and accessible from a terminal.

Double-click Docker for Windows Installer to run the installer.

When the installation finishes, Docker starts automatically. The whale in the notification area indicates that Docker is running, and accessible from a terminal.

Once Docker is installed, download the image containing the IgPipeline on https://hub.docker.com/r/stratust/igpipeline

Open up a terminal session and download the image using the command docker pull stratust/igpipeline

In Desktop, create a folder named "ig_analysis". Inside this folder, download and extract the zip file available through this link and create a folder named "results"

• To load a container with the downloaded image, open up a terminal session and type:

docker run -it -v ~/Desktop/ig_analysis/data:/igpipeline/data -v ~/Desktop/ig_analysis/results:/igpipeline/results stratust/igpipeline:latest

• Right after the container is loaded, to start the pipeline execution type:

snakemake --until SHM

• In the hydrophobicity analysis we calculate the GRAVY score for 22,654,256 IGH CDR3 sequences from a public database of memory B-cell receptor sequences (doi:10.1371/journal.pone.0160853), which requires plenty of computing resources and it takes ~30 min to execute. Using the command provided above this step WILL NOT be executed. If you want to execute the hydrophobicity score calculation, run the pipeline with the command snakemake

• If you have enough computing resources to parallelize the execution, specify the parameter -j < number_of_cores > for the snakemake.

That's it ! The IgPipeline is executing.

Once the execution finishes, the results will be available in the folder "results"