Prowler

Prowler trims Oxford Nanopore Technologies (ONT) long-read sequence data by applying a window-based algorithm that replaces low-quality segments with 'N' bases to preserve phase and read length for downstream analyses such as alignment and assembly.

Key Features:

• Window-based trimming: Evaluates base quality in sliding windows across reads to identify low-quality segments.
• 'N' base replacement: Replaces trimmed sections with 'N' bases instead of discarding them, maintaining original read length and positional information.
• Phase and read-length preservation: Retains phase information and read-length context important for downstream analyses like phasing, alignment, and assembly.
• Improved downstream metrics: Demonstrates reduced error rates, increased numbers of mapped reads, and improved assembly contiguity relative to traditional tools such as Nanofilt.
• Short-read algorithm inspiration: Adopts concepts from short-read sequencing algorithms to process long-read ONT data more accurately.

Scientific Applications:

• Sequence alignment and genome assembly: Used to improve read mapping quality, reduce assembly errors, and enhance contiguity in genome assemblies generated from ONT data.

Methodology:

Processes long-read sequences using a window-based trimming approach inspired by short-read sequencing algorithms and replaces low-quality segments with 'N' bases to preserve phase and read length.