Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the
computational challenge of efficiently and accurately constructing multiple genome …

Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete
sequence of a human genome. To resolve the most complex repeats, this project relied on …

We present several recent improvements to minimap2, a versatile pairwise aligner for
nucleotide sequences. Now minimap2 v2. 22 can more accurately map long reads to highly …

INTRODUCTION Modern genomics depends on inexpensive short-read sequencing.
Sequenced reads up to a few hundred base pairs in length are computationally mapped to …

Although Kraken'sk-mer-based approach provides a fast taxonomic classification of
metagenomic sequence data, its large memory requirements can be limiting for some …

Abstract Approximately 5–10% of the human genome remains inaccessible due to the
presence of repetitive sequences such as segmental duplications and tandem repeat arrays …

Motivation The emergence of high-throughput sequencing technologies revolutionized
genomics in early 2000s. The next revolution came with the era of long-read sequencing …

Motivation Recent advances in sequencing technologies promise ultra-long reads of∼ 100
kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs …

We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG
combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over …