sequ-into

sequ-into detects and flags impurities, contamination, and off-target sequences (ICOs) in Oxford Nanopore MinION sequencing data to enable early identification and mitigation of non-target reads.

Key Features:

• Early detection: Identifies ICOs during the initial stages of a MinION sequencing run to reduce sequencing of non-target material.
• ICO database comparison: Compares sequencing reads against a predefined database of ICO sequences to detect known contaminants.
• Real-time flagging: Flags potential contaminants and off-target reads during the run for immediate review.
• Low computational requirement: Operates with low resource demands to enable deployment on limited infrastructure.
• Actionable outputs: Produces flags and insights intended to inform library preparation adjustments and conservation of sequencing capacity.

Scientific Applications:

• Contamination screening: Detection of human DNA/RNA contamination in sequencing samples.
• rRNA depletion assessment: Identification of residual rRNA sequences that indicate insufficient rRNA depletion.
• Bacteriophage and prokaryotic sample QC: Detection of residual host organism DNA/RNA in bacteriophage cultivation and other prokaryotic samples.
• Sequencing capacity optimization: Informing decisions to adjust library preparation and conserve or reuse MinION flow cell capacity.

Methodology:

sequ-into compares sequencing data in real time against a predefined database of ICO sequences and flags reads matching known contaminants or off-targets during a MinION run.