If MongoDB is local, python clonify.py -d <database> will iteratively run Clonify on all collections in the specified database.
For remote databases, and to specify a single collection:
python clonify.py -i <MongoDB IP> -p <MongoDB port> -d <database> -c <collection>
To run Clonify without updating the target MongoDB with lineage information and instead writing basic lineage information to an output file:
python clonify.py -i <MongoDB IP> -p <MongoDB port> -d <database> -c <collection> -o <output_file> -n
By default, Clonify will group sequences by variable gene family and separately assign lineages within each group. To group by variable gene instead of variable gene family:
python clonify.py -d <database> -s gene
To run Clonify on the entire dataset without grouping by gene or family (NOTE: this can be slow and very memory intensive):
python clonify.py -d <database> -s none
Briney, B., Le, K., Zhu, J., and Burton, D.R. (2016). Clonify: unseeded antibody lineage assignment from next-generation sequencing data. Sci. Rep. 6, 23901.
Raw data used in the Clonify paper (Briney et al, 2016) can be found at https://github.com/briney/clonify-scirep2016data
python >=2.7
numpy
scipy
biopython
pymongo
python-levenshtein
fastcluster
all package requirements can be installed with pip:
pip install <package>