Sequali

Sequali performs comprehensive quality control on short- and long-read sequencing data by identifying adapter sequences, overrepresented sequences, and duplicates to support downstream analyses.

Key Features:

• Adapter Search: Identifies and reports adapter sequences present in sequencing reads.
• Overrepresented Sequence Analysis: Detects and characterizes overrepresented sequences to reveal biases or contaminants.
• Duplication Analysis: Identifies duplicate reads to assess redundancy and potential PCR artifacts.
• Support for Multiple Input Formats: Accepts FASTQ and uBAM file formats for both short- and long-read datasets.
• High-performance Implementation: Implements performance optimizations using Python with C extensions to accelerate processing.

Scientific Applications:

• Cross-platform sequencing QC: Performs quality control for datasets from short-read and long-read technologies, including Oxford Nanopore Technologies.
• Variant calling preparation: Produces QC metrics and filtered reads to improve reliability of variant calling workflows.
• Genome assembly preprocessing: Identifies contaminants and duplicates to improve accuracy of genome assembly.
• Transcriptome profiling QC: Detects sequence-level artifacts that can affect transcriptome quantification and analysis.

Methodology:

Implemented in Python with C extensions to improve performance and reported to operate faster than comparable quality control programs for short- and long-read sequencing.