BRILIA: Integrated tool for high-throughput annotation and lineage tree assembly of B-cell repertoires

Donald W. Lee-1, Ilja Khavrutskii-1, Anders Wallqvist-1, Sina Bavari-2, Christopher L. Cooper-2, and Sidhartha Chaudhury-1*

1-Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, USA

2-Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA

*-Corresponding author: [email protected]

BRILIA is designed to annotate a repertoire of B-cell receptor sequences across the VDJ junction. It returns the CDR3 regions, VDJ germline gene predictions, and also phylogeny relationships among B cells. For more information on how BRILIA works, please read the methods article cited above.

Takes fasta, fastq, csv, xlsx, or xlsx file containing the sequenceID (SeqName or SeqNum), sequence (nucleotide or Seq), and template count (TemplateCount) data.

Returns a tabulated spreadsheet or CSV file listing the annotation results and phylogeny relationships among sequences. Will create and save to a new folder call BRILIAvXX, where "XX" is the version number (currently 13).

1. Copy all codes into a folder called BRILIA.

2. Open MATLAB, find the BRILIA folder, and run in the command line "addAllPaths". This will add all folders and subfolders to the MATLAB path.

3. Type "BRILIA" in the command line and follow instructions. You can also use "BRILIAbatch" instead to process multiple files.

4. Select the input file to process (try the example input files shown in the Example folder).

5. BRILIA should create a new folder called BRILIAvXX and save the output results in tabulated format.

The program is distributed under the GNU General Public License [http://www.gnu.org/licenses/gpl.html].

2016-12-22: Here are a list of updates that we are currently working on.

• Better error handling to prevent BRILIA from stopping due to one sequence
• Extra input sequence formatting and trimming features so that users don't have to do this
• Detailed code comments for readability
• Removing dependency on using Excel file reader and writer to increase usability
• Easier switching between human and mouse database searches