III: Small: Improving de novo genome assembly using single-copy k-mers

A genome is the complete set of deoxyribonucleic acid (DNA) in an organism and contains all of the instructions required for that organism to function. Obtaining access to the entire genomic sequence of a species, which is called genome sequencing, can enable life scientists and medical researchers to understand the causes of diseases, develop personalized medicine, identify genetic variations within populations, study evolution, and develop new treatments or cures for diseases. Due to technological limitations of DNA sequencing instruments, scientists can only read a limited amount of DNA and not entire chromosomes. As a consequence, scientists have to break the genome into fragments before reading each fragment using a sequencing instrument. Once fragments are sequenced, they need to be assembled together like a puzzle that contains billion of pieces. This problem is called genome assembly, which is the focus of this research project. Due to complexity of solving this problem, the organisms sequenced so far represent a minuscule proportion of those that inhabit our planet, many of which we depend on for our food or against which we must defend to sustain human society. The long-term impact of obtaining the genome of a new species can be profound and impactful once the sequence becomes a routine component of practical problem solving and downstream analyses for the scientific community. This project focuses on developing new methods that would allow a much more accurate and efficient genome assembly for many organisms. The problem of genome assembly is one of the most studied problems in computational biology, yet it remains computationally challenging due to the high repetitive content of eukaryotic genomes, short read length, uneven sequencing coverage, non-uniform sequencing errors, and chimeric reads. As exemplified by the 20-year timeframe to obtain the last 8% of the human genome, producing a telomere-to-telomere gapless assembly still requires a substantial amount of resources, which are typically not available to the average lab. This research project focuses on closing assembly gaps, i.e., the problem of reconstructing correctly the repetitive sequences which are usually the hardest to assemble. The research plan includes the following tasks. (i) Develop a de novo repeat assembly method for Hi-Fi reads based on single-copy k-mers (ii) Develop a haplotype-aware repeat assembly method for Hi-Fi reads based on single-copy k-mers (iii) Develop a de novo assembly method for ultra-deep HiFi reads. The proposed solutions will involve the innovative use of single-copy k-mers (fixed length, variable length, homopolymer-compressed) and the design of new combinatorial algorithms for phasing and iterative meta-assembly. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.