Align sequences and then parse features.
alignparse is a Python package written by the Bloom lab.
This package 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.
The source code is on GitHub.
See the alignparse documentation for details on how to install and use alignparse.
To contribute to this package, read the instructions in CONTRIBUTING.rst.
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