read_it_and_keep

Read-it-and-Keep: Targeted filtering of SARS-CoV-2 sequencing reads

Read-it-and-Keep filters high-throughput sequencing datasets to retain reads matching the SARS-CoV-2 genome while removing contaminating human DNA, enabling motif-based and region-specific read selection from Illumina and nanopore data.

Key Features:

• Targeted Read Retention: Retains reads matching the SARS-CoV-2 genome to ensure exclusion of human genomic sequences.
• PolyA Tail Exclusion Strategy: Excludes the viral polyA tail from the reference genome to prevent retention of human reads that could arise from mapping against full human genome references.
• Sequencing Platform Compatibility: Processes both Illumina and nanopore sequencing data formats.
• Low Memory Footprint: Maintains peak RAM usage below 10 MB and completes processing in under one minute.
• C++ Implementation: Implemented in C++ for high-performance read processing.

Scientific Applications:

• Human Read Decontamination: Removes contaminating human reads from SARS-CoV-2 sequencing datasets to enable compliant data sharing and analysis.

Methodology:

Performance validated using comprehensive datasets including all possible reads from the human genome, samples representing 26 populations from the 1000 Genomes Project, and diverse SARS-CoV-2 genomes to ensure robust discrimination between viral and human sequences.