aairr16

Analysis of adaptive immune receptor repertoires (2016) course slides and notes.

Cloning this repository

This repository contains large sequence and tabular files stored using Git-LFS, which can be installed from here.

Once the lfs subcommand is installed, the repository can be cloned as follows.

git lfs clone https://github.com/antibodyome/aairr16

Required software

General requirements

You will need to have the following installed on your computer:

• Python 3
• R
• Java
• wget

EDirect

Entrez Direct, or EDirect, allows programmatic access to NCBI. It is available for download from ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/.

SRA Toolkit

The SRA Toolkit from NCBI allows downloading of datasets from NCBI SRA to FASTQ files stored locally. It can be downloaded from https://github.com/ncbi/sra-tools/wiki/Downloads.

IgBLAST

IgBLAST compares reassorted BCR/TCR sequences against a germline database using a modified version of BLAST. It is available from ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/.

vdjtools

vdjtools analyses CDR3 regions, and is well suited for TCR analyses. Installation instructions can be found at http://vdjtools-doc.readthedocs.io/en/latest/install.html.

phylip

dnapars from the phylip suite of programs is used for inference of lineage trees in the R library alakazam. It can be downloaded from http://evolution.genetics.washington.edu/phylip.html, but is also available from package managers.

Python packages

This course makes heavy use of Jupyter notebooks. You will need to install Jupyter e.g.

pip3 install notebook

The slides make use of the RISE extension:

pip3 install RISE
jupyter-nbextension install rise --py --sys-prefix
jupyter-nbextension enable rise --py --sys-prefix

--sys-prefix can be replaced by --user or --system depending on the type of installation desired.

Depending on taste, you may prefer to use a bash kernel for some tasks.

pip3 install bash_kernel
python3 -m bash_kernel.install

In addition, the following packages are required (and can be installed using pip)

• rpy2
• biopython
• pandas
• matplotlib
• presto
• changeo

Whilst not a package, but rather a set of Python scripts, @williamdlees TRIgS will be used as a simple interface to analyse immunoglobulin sequences:

https://github.com/williamdlees/TRIgS

R packages

• ggplot2
• igraph
• dplyr
• alakazam
• shazam

In addition, an R kernel for Jupyter is also required. In R:

install.packages(c('repr', 'IRdisplay', 'crayon', 'pbdZMQ', 'devtools'))
devtools::install_github('IRkernel/IRkernel')
IRkernel::installspec()  # to register the kernel in the current R installation