Genome assembly algorithms articles from across Nature Portfolio

In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining challenges in resolving highly repetitive sequences and polyploid genomes.

High-quality genome assemblies of grain and vegetable cowpeas and re-sequencing of 344 accessions characterize genomic variations between cowpea subspecies and their domestication and improvement under selection.

Haplotyping is the process of distinguishing alleles inherited together on a chromosome, a crucial step in assembling and interpreting genome sequences. Here, the authors present a computationally efficient haplotype assembly tool for long read sequencing data.

Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, the authors present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads.

Diploid assembly is a difficult task that requires several types of genomic sequencing data, including — but not limited to — HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.

Shinichi Morishita recalls a seminal publication by Weber and Myers, who in 1997 proposed a direct whole-genome shotgun sequencing approach to tackle the human genome.

We present an analysis that shows that although nearly half of the human genome comprises repetitive sequences, recombination between homologous repeats has a minor role in cancer chromosomal evolution.

The release of the first telomere-to-telomere (T2T) human genome sequence marks a milestone for human genomics research and holds promise of complete genomes for evolutionary genomic studies. Here we describe the advances that this new human genome assembly represents and explore the potential insights that the complete genome sequence could bring to evolutionary genomics. We also discuss the potential challenges to be faced in applying this new sequencing strategy to a broad spectrum of extant species.

A repeat-aware pipeline corrects structural assembly errors and polishes assembly sequences in large repeats without overcorrection.