readfish

Readfish: Targeted nanopore sequencing via real-time selective sequencing

Readfish enables targeted sequencing of gigabase-scale genomes on nanopore platforms by performing real-time sequence mapping and voltage-controlled selective sequencing to enrich or deplete specific DNA molecules.

Key Features:

• Selective Sequencing: Reverses voltage across individual nanopores to reject or retain DNA molecules, enabling targeted enrichment or depletion without prior knowledge of sample composition.
• GPU Base-Calling Integration: Utilizes graphical processing unit (GPU)–accelerated base-calling to replace dynamic time warping, improving scalability and real-time mapping against gigabase-sized references.
• Chromosome Enrichment: Enriches specific human chromosomes and low-abundance organisms within mixed populations.
• Targeted Gene Panels: Targets panels including 25,600 exons from 10,000 human genes and 717 cancer-related genes; detects PML-RARA fusions in the NB4 cell line within 15 hours of sequencing.

Scientific Applications:

• Human Genetics and Cancer Genomics: Performs rapid enrichment of defined genomic regions and structural variants for large-genome and oncology-focused studies.
• Metagenomics: Enriches low-abundance organisms within complex microbial communities.

Methodology:

Readfish conducts real-time base-calling using GPU acceleration, maps reads to a reference genome, and dynamically controls nanopore voltage to accept or reject DNA strands. This approach enables scalable targeted sequencing of large genomes without specialized sample preparation.