GC replay

This repository contains the code and data for the analysis of B cell receptor (BCR) sequences isolated in Germinal Center (GC) - Replay experiments.

For more details, please see the analysis website.

Reproduce analysis

Install Nextflow by using the following command:

$ curl -s https://get.nextflow.io | bash

Download the Docker Desktop, there exists several distributions packaged for various linux flavors

$ curl -fsSL https://get.docker.com -o get-docker.sh && sudo sh get-docker.sh

Note: the Dockerfile contains all the required dependencies. Add the -profile docker to enable the containerized execution to the example command line shown below.

Launch the pipeline execution with the following command:

$ git clone [email protected]:matsengrp/gcreplay.git && cd gcreplay
$ nextflow run main.nf -profile docker -resume

GC Metadata

The metadata for germinal centers analyzed across all replay experiments is stored in this file. The columns are as follows:

• uid: (unique identifier) This is in the format of D<imm_duration>_M<mouse>_GC<gc>.
• ngs_id: (ngs file id) reference to associated sequencing run specified in ngs_manifest.csv.
• imm_duration: (immunization duration) This is the number of weeks after immunization that the sample was taken.
• mouse: (mouse number) This is the unique identifier for the mouse.
• gc: (germinal center number) This is the unique identifier for the germinal center.
• strain: (mouse strain) This is the strain of the mouse.
• node: (lymph node number) This identifies the specific lymph node location in the mouse.
• cell_type: (cell type) This is the type of cell that was sequenced.
• plate: (plate barcode) This is the barcode of the plate that the sample was sequenced on.
• hc_barcode : (heavy chain barcode) This is the barcode of the heavy chain.
• lc_barcode : (light chain barcode) This is the barcode of the light chain.
• row : (well rows) Which rows of the 96-well plate contain the sample.
• col : (well columns) Which columns of the 96-well plate contain the sample.

Building docs

We use pixi to manage dependecies. To build the documentation, first install pixi:

$ curl -fsSL https://pixi.sh/install.sh | bash
$ cd gcreplay
$ pixi install

Then, run the following command to build the documentation:

$ docs