abstar

VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.

• Source code: github.com/brineylab/abstar
• Documentation: abstar.readthedocs.org
• Download: pypi.python.org/pypi/abstar
• Docker: hub.docker.com/r/brineylab/datascience/

install

pip install abstar

use

To run abstar on a single FASTA or FASTQ file, you need to supply the input file and the project directory (into which output and logs will be written):

abstar path/to/sequences.fasta path/to/project_directory

To iteratively run abstar on all files in an input directory, pass a directory containing FASTA or FASTQ files instead of the path to a single file:

abstar path/to/input_directory path/to/project_directory

additional options

abstar contains a number of additional options and tools, including merging paired-end reads, parsing unique molecular identifiers (UMIs), and building/using custom germline databases. These are described in the abstar documentation.

api

Most core abstar functions are available through a Python API, making it easier to run abstar as a component of integrated analysis pipelines or to run abstar interactively (e.g. in a Jupyter notebook). See the abstar documentation for more detail about the API.

testing

You can run the complete abstar test suite by first installing pytest:

pip install pytest

followed by:

git clone https://github.com/brineylab/abstar
cd abstar
pytest

This test suite is automatically run after every commit, and is tested against all supported versions of Python.

requirements

Python 3.10+

abutils
click
matplotlib
numpy
pandas
parasail
polars
pyarrow
pytest