bitags 0.1.0

Fast and flexible suite of operations for barcoded NGS reads.

bitags

Fast and flexible suite of operations for barcoded NGS reads.

Warning: This package is in early alpha. The API may change without notice and it is not yet recommended for production use.

About

Bitags is a package designed to simplify working with barcoded NGS reads. It relies on an adapted version of the bitap algorithm to perform fuzzy matching of tags composing a barcode (usually from a combinatorial barcoding method). Moreover, it provides additional utility functions for barcoded reads.

Currently supported features:

• Barcoding — identify and assign barcodes to reads using fuzzy bitap matching
• Trimming — trim reads based on a barcoding schema
• Classification — classify reads according to a barcoding schema
• Manipulation — embed barcodes, convert paired to unpaired reads
• I/O — read and write FASTQ files via lazy Polars DataFrames
• Visualization — visualize read structure in terminal, html or png.

Bitags can be used as a command line tool or through the Python API.

Installation

pip install bitags

Or from source by cloning and using maturin to build.

Usage

Proper documentation will be available soon, for now please rely on docstrings.

Cite

At the moment, there is no paper on Bitags. If you find this package useful for your work, please cite it by providing the link to the GitHub page.

License

BSD 3-Clause License. See LICENSE for details.