Genome assembly algorithms articles from across Nature Portfolio

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.

JaBbA v1 pinpoints the ‘loose ends’ of large (>10-kb) unmapped structural variants in short-read DNA sequencing, suggesting that about 90% of cancer chromosomal alterations outside centromeres are resolvable with short reads and that long reads will primarily improve calling of smaller somatic variants.

Breakage-fusion-bridge (BFB) is a mechanism that leads to complex genome rearrangements in multiple cancers. Here, the authors develop a computational method for identifying these events, even when further complicated by additional structural variations.

Resistance to carbapenems, a class of last-line antibiotics, is a global health threat. This study analysed a two-decade history of carbapenem resistance and identified complex, multi-level (bacterial strain, plasmid, gene) transmission dynamics.

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.

Scallop2, a tool that enables accurate reference-guided transcriptome assembly, capitalizes on recent developments in short-read sequencing protocols for single-cell RNA sequencing by leveraging multi-end and paired-end information.

Method development is indispensable for obtaining complete genomes, and deciphering them.

Phased genomes from diverse human populations are assembled using multiple sequencing technologies.