SequelTools

SequelTools performs quality control, read subsampling, and read filtering for raw PacBio Sequel long-read sequence data to generate statistics and plots for downstream genomic analyses.

Key Features:

• Quality Control (QC): Processes raw sequence data from multiple SMRT cells and produces statistics and publication-quality plots including N50, read length and count statistics, Pulse Signal Ratio (PSR), and Zero-Offset Rate (ZOR).
• Read Subsampling: Subsamples reads by selecting the longest subreads per Circular Consensus Read (CLR) or by random CLR selection.
• Read Filtering: Filters out low-quality scraps reads and applies a minimum CLR length threshold to normalize datasets for downstream analysis.

Scientific Applications:

• Genome Assembly and Annotation: Provides high-quality filtered long reads to support accurate genome assembly and annotation.
• Epigenetic Studies: Supports detection of methylated bases in PacBio Sequel data for epigenomic analyses.
• Structural Variant Detection: Provides high-fidelity long reads suitable for identifying structural variants within genomes.

Methodology:

Implemented using bash, R, and Python and relying only on standard libraries and packages.