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Examples
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The `alignparse `_ package is designed to aid in the analysis of long-read sequencing of user-defined amplicons. Major functionaly includes:
- The :class:`alignparse.targets.Targets` class for defining reference sequence `Targets`, aligning reads, and parsing features from aligned reads.
- The :mod:`alignparse.consensus` for analyzing mutations and sequencing accuracy, especially for sequences grouped by shared barcodes.
Here are some examples that demonstrate how to utilize this functionality and other aspects of the `alignparse `_ package:
.. toctree::
:maxdepth: 1
recA_DMS
lasv_pilot
flu_virus_seq_example
The actual notebooks and input files used in these examples are `available here `_.
The above examples can also be run as interactive Jupyter notebooks on `mybinder `_ by going to the `following link `_ (it may take a minute to load) and then opening the notebook you want to run.