alignparse documentation

alignparse is a Python package written by the Bloom lab. It is designed to align long sequencing reads (such as those from PacBio circular consensus sequencing) to targets, filter these alignments based on user-provided specifications, and parse out user-defined sequence features.

For each read that passes the user-defined filters, the user can define what information about each feature (e.g. sequence, mutations, and sequencing accuracy) should be retained for further analyses. The alignparse.consensus module provides tools for such further analyses, including analyzing mutations identified in sequence features and defining consensus sequences from barcoded sequencing reads.

The alignparse source code is freely available on GitHub.

If you use alignparse for your work, please cite the references in Acknowledgements.

See below for information and examples of how to use this package.