Genome Assembly Algorithms

Currently, research has entered the genomic era. The high-throughput sequencing of short reads and long reads has increased, while the cost has decreased. Most of the key genomes have been sequenced, and an increasing number of reference genomes from uncommon species are currently in progress toward completion. What is more, a lot of finished draft genomes have been progressively refined and updated to achieve complete, telomere-to-telomere assemblies. Algorithms primarily focus on de novo assembly, evolving from Overlap-Layout-Consensus (OLC) for Sanger reads, to De Bruijn Graphs (DBG) for short reads, and back to OLC for PacBio or nanopore long reads. Scaffolding facilitates chromosome-level assembly, and graph-based algorithms enable pangenome assembly, which is poised to become a new standard for genomic references. A wide variety of genome assembly software has been extensively adopted, efficiently conserving computational resources while improving genome quality.