alignparse

alignparse parses features from long-read sequencing reads (including PacBio circular consensus sequencing reads) and aligns them to user-specified target sequences to extract user-defined sequence features such as mutations, unique molecular identifiers, and cell barcodes for downstream analyses.

Key Features:

• Alignment of Long Reads: Aligns long sequencing reads, including PacBio circular consensus sequencing reads, to specified target sequences such as PCR amplicons.
• User-Specified Filtering: Filters alignments based on custom user specifications and thresholds.
• Parsing Complex Features: Parses user-defined sub-sequence features from aligned reads, including mutations, unique molecular identifiers (UMIs), cell barcodes, and flanking sequences.
• Flexible Target Specification: Accepts target sequences in GenBank Flat File format containing an arbitrary number of annotated sub-features.
• Customizable Feature Extraction: Extracts sequences, mutations, and sequence quality (accuracy) with configurable, per-feature thresholds.

Scientific Applications:

• Influenza Virus Mutation Identification: Identifies mutations in influenza virus sequences, including within single cells.
• Deep Mutational Scanning: Associates barcodes with gene mutants to support deep mutational scanning experiments.

Methodology:

Aligns long reads to target sequences, filters alignments by user specifications, parses sub-sequence features defined in GenBank Flat Files, and extracts sequences, mutations, and quality (accuracy) metrics with per-feature thresholds.