Genome Informatics Section

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

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News

Verkko2 is released!

January 2, 2025

We are excited to announce that Verkko2 is now available! Not only is it 4x faster than Verkko1, this version adds support for proximity ligation data (e.g. Hi-C, Pore-C) for T2T phasing and scaffolding without the need for trios. Our latest preprint describes the new methods and results: “Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding”. With these improvements, Verkko2 can now assemble, on average, around 40 out of 46 diploid human chromosomes as T2T scaffolds (and ~20 as T2T contigs), including the most difficult to assemble acrocentric chromosomes. However, these improvements are not limited to human genomes and Verkko2 should work well for any diploid or haploid genome (polyploids are a work in progress). We look forward to enabling many more T2T genomes in 2025!

The NHGRI Center for Genomics and Data Science Research is hiring!

August 13, 2024

Join our team and contribute to the development of complete, personalized “telomere-to-telomere” (T2T) genome assemblies and the analysis of previously inaccessible regions of the genome! We are currently accepting applications for center coordinator, bioinformatics engineer/scientist, and postdoctoral researcher.

Publications
Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes
Gigascience, January 6, 2025
Zhou Y, Jin J, Li X, Gedman G, Pelan S, Rhie A, Jiang C, Fedrigo O, Howe K, Phillippy AM, Jarvis ED, Grutzner F, Zhou Q, Zhang G
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
bioRxiv, December 17, 2024
Billingsley KJ … Rhie APhillippy AM … Blauwendraat C
Software

Canu

A single molecule sequence assembler for genomes large and small

Mash

Fast genome and metagenome distance and containment estimation using MinHash

Krona

Interactively explore metagenomes and more from a web browser