``alignparse`` documentation
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`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.
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installation
examples
alignparse
package_index
acknowledgements