• BASIC was developed and tested using Python 3.4.4 and 2.7.10
• BASIC requires Bowtie2 to run.
• The db/ folder must remain with the BASIC.py file

python BASIC.py -b <path_to_Bowtie2> -PE_1 <R1.fastq.gz> -PE_2 <R2.fastq.gz> -g <species> -i <receptor>

Parameters

• species: "human" or "mouse"

  Note: other species are possible by adding the appropriate bowtie2 indices and following the existing db/ directory structure

• receptor: "BCR" or "TCR"

For more advanced usage or other use cases e.g. single end reads:

python BASIC.py -h

http://ttic.uchicago.edu/~aakhan/BASIC/

1.3.1 (2018/06/27)

• Please contact Aly Azeem Khan [email protected] for any questions or comments.
• More recent updates to BASIC have been contributed by Derek Croote [email protected]

Software provided to academic users under MIT License