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 filters, information about the features (e.g. accuracy, sequence, mutations) is retained for further analyses.

See the alignparse documentation for details on how to install and use alignparse.

Please cite alignparse if you use it in your work.

The source code is on GitHub.

To contribute to this package, read the instructions in CONTRIBUTING.rst.

To report issues or seek support, please use the GitHub issue tracker.