BASIC: BCR and TCR assembly from single cell RNA-seq

Prerequisites

• BASIC is tested to work on Python 2.7 and 3.5+
• BASIC requires Bowtie2 to run.
• The db/ folder must remain with the BASIC.py file

Installation

BASIC can be installed with bioconda. Once conda and bioconda are set up, running the following will install BASIC and Bowtie2:

conda install basic

Alternatively, if you would like to use the development version and have Bowtie2 installed, this repository can be cloned and BASIC can be run as shown below.

Usage

BASIC.py [-h] [-i TYPE] [-p NUM_THREADS] [-n NAME] [-SE FASTQ]
                [-PE_1 LEFT] [-PE_2 RIGHT] [-g GENOME] [-b BOWTIE] [-t TMPDIR]
                [-o OUTPUT_LOCATION] [-a] [-v] [-d DATABASE_PATH]
                [--subsample SUBSAMPLE] [--version]

  -h, --help            show this help message and exit
  -i TYPE               Type of receptor. Choices: "BCR" or "TCR" (default:
                        BCR)
  -p NUM_THREADS        Launch p > 2 threads that will run on separate
                        processors/cores (default: 2)
  -n NAME               Name of output file. Note: a ".fasta" extension will
                        be added (default: result.fasta)
  -SE FASTQ             Single end FASTQ file (optionally gzipped). (example:
                        se.fastq)
  -PE_1 LEFT            Paired end (left) FASTQ file (optionally gzipped).
                        -PE_2 is required and pairs must match order.
                        (example: pe_1.fastq)
  -PE_2 RIGHT           Paired end (right) FASTQ file (optionally gzipped).
                        (example: pe_2.fastq)
  -g GENOME             Options: "human" or "mouse" (default: human). Note:
                        other species are possible by adding the appropriate
                        Bowtie2 indices and following the existing db/
                        directory structure
  -b BOWTIE             Absolute path to bowtie2 executable or directory
                        containing it
  -t TMPDIR             Path to directory for writing intermediate files.
                        (default: current working directory)
  -o OUTPUT_LOCATION    Output directory (default: current working directory)
  -a                    Allow for partial reconstruction i.e. do not terminate
                        if one or both chains do not assemble.
  -v                    Turns on verbosity for more details.
  -d DATABASE_PATH      Path to database directory. Defaults to <path of
                        BASIC.py>/db
  --subsample SUBSAMPLE
                        Use the first <int> number of reads of the input.
                        Default: no limit
  --version             show program's version number and exit

Paired-end reads example

BASIC.py -b <path_to_Bowtie2> -PE_1 R1.fastq.gz -PE_2 R2.fastq.gz -g human -i BCR

More information

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

Version

1.5.0 (2019/07/11)

Publication

BASIC: BCR assembly from single cells.
Canzar S, Neu KE, Tang Q, Wilson PC, Khan AA
Bioinformatics, Volume 33, Issue 3, 1 February 2017.

Contact

• Please contact Aly Azeem Khan aakhan@ttic.edu for any questions or comments.
• More recent updates to BASIC have been contributed by Derek Croote dcroote@stanford.edu

License

Software provided to academic users under MIT License