VIsualizing BCR repertoires and intraCLonal Diversity

ViCloD is a web server for visualizingz the clonality and intraclonal diversity of BCR repertoires. Here we make the ViCloD pipeline available, the stand-alone version. Users can run it locally and visualize their results online. This pipeline uses the following tools: MobiLLe to cluster the clonally-related sequences in BCR repertoires and ClonalTree to reconstructing the evolutionary history of a BCR lineages.

REFERENCE Lucile Jeusset, Nika Abdollahi, Anne Langlois De Septenville, Marine Armand, Thibaud Verny, Clotilde Bavetti, Frédéric Davi and Juliana S. Bernardes. ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intra-clonal diversities in B-cell tumors. To be submitted.

CONTACT E-mail: juliana.silva_bernardes@sorbonne-universite.fr

• An AIRR formatted file containing annotated IGH sequences.
• See example input file

• ViCloD returns:

  • [repertoire_name]_visualization.zip : contains all the files necessary for viewing the BCR repertoire in the format requested by the ViCloD website (compressed file)

  • [repertoire_name]_repertoire.json : the clustering output of clonally-related sequences of the repertoire in JSON format

  • [repertoire_name]_tree_all.json : the reconstructed BCR lineage tree of the 5 first clones in JSON format

  • [repertoire_name]_tree_simplification1.json : the first level of simplification of the previously reconstructed BCR lineage tree in JSON format

  • [repertoire_name]_tree_simplification2.json : the second level of simplification of the previously reconstructed BCR lineage tree in JSON format

  • [repertoire_name]_C[clone_number]_HAUS_sequence.fasta : a fasta file containing the HAUS sequence of the indicated clone

  • [repertoire_name]_C[clone_number]_subclones_sequences.fasta : a fasta file containing the subclone sequences of the indicated clone

  • [repertoire_name]_log.txt : contain the information on the reads used for the analysis.

  • [repertoire_name]_unannotated_seq.txt : contains all the sequences of the input AIRR file which are not correctly annotated to allow analysis by ViCloD

  • [repertoire_name]_AIRR_seq_name_matching.txt : contain the match between the original name of the reads (in AIRR file) and the new id provide by ViCloD

  • [repertoire_name]_unique_seq_id_matching.txt : ids of sequences with the same nucleotide sequence

• See example output files

• We strongly recommend anaconda environment.

• Python version 3 or later

• numpy :

  conda install numpy
  

  or

  pip install numpy
  

• matplotlib

    conda install -c conda-forge matplotlib
  

  or

  pip install matplotlib
  

• Palettable :

  conda install -c conda-forge palettable
  

  or

  pip install palettable
  

• skbio

  conda install -c anaconda scikit-bio
  

  or

  pip install scikit-bio
  

• Levenshtein

  conda install -c conda-forge python-levenshtein 
  

  or

  pip install python-Levenshtein
  

• Biopython

  conda install -c conda-forge biopython
  

  or

  pip install biopython
  

• ete3 :

  conda install -c etetoolkit ete3
  

  or

  pip install ete3
  

• python-newick :

  conda install -c bioconda python-newick
  

  or

  pip install newick
  

• muscle :

  conda install -c bioconda muscle
  

  or

  pip install muscle
  

The command line for launching the ViCloD is:

$ run_ViCloD.sh [AIRR_file] [output_path] [threshold_value] [thresold_type]

• [AIRR_file] is the AIRR file containing the annotated sequences of the BCR repertoire,
• [output_path] is path of the ouptut directory
• [threshold_value] is a threshold for eliminating infrequent reads
• [thresold_type] is the type in which the threshold value is given (percentage or number)

For instance the following command can be run in the src/ folder:

$ src/run_ViCloD.sh Examples/Input/example.tsv Examples/Output 0 number

Output files will be placed in a folder as such:

[output_path]/[AIRR_file_name]_ViCloD_output

• [AIRR_file_name] is the name of the AIRR file provide as input

• The program is distributed under the CeCILL licence
• Feature requests and open issues.