BleTIES

BleTIES predicts, assembles, and analyzes internally eliminated sequences (IESs) in ciliate genomes using Pacific Biosciences and Oxford Nanopore long-read data to characterize DNA elimination and improve ciliate genome assemblies.

Key Features:

• Prediction: Predicts IES locations from mapped long reads.
• Assembly: Assembles IES sequences to enable reconstruction of longer IESs.
• Analysis of excision patterns: Analyzes IES excision patterns and detects correlations between neighboring element eliminations.
• Long-read support: Supports Pacific Biosciences (PacBio) and Oxford Nanopore Technologies long-read sequencing data.
• Repetitive and low-complexity regions: Enables reconstruction and analysis of IESs that contain repetitive or low-complexity sequences.
• Implementation: Implemented in Python 3.
• Tool suite: Provides a suite of tools for detecting, assembling, and analyzing IESs from mapped long reads.
• Benchmarking: Benchmarked on published sequence data.

Scientific Applications:

• DNA elimination studies: Characterizing mechanisms of DNA elimination and IES excision in ciliates.
• Genome assembly improvement: Improving the accuracy and completeness of ciliate macronuclear genome assemblies by resolving IESs.
• Genomic architecture: Investigating correlations between neighboring IES eliminations to study ciliate genomic architecture.

Methodology:

Uses mapped Pacific Biosciences and Oxford Nanopore long reads for prediction, assembly, and analysis of IESs; implemented in Python 3 and validated using published sequence data.