Examples

The alignparse package is designed to aid in the analysis of long-read sequencing of user-defined amplicons. Major functionaly includes:

• The alignparse.targets.Targets class for defining reference sequence Targets, aligning reads, and parsing features from aligned reads.

• The 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:

• RecA deep mutational scanning libraries
• Lassa virus glycoprotein PacBio sequencing
• Single-cell virus sequencing

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.