CD Genomics

How much human structural variation are short reads missing? Significantly more than we realized, according to a large-scale study published in Nature (2025).

Schloissnig, Korbel and colleagues applied Oxford Nanopore long-read sequencing to 1,019 samples from the 1000 Genomes Project — generating the most comprehensive long-read SV map to date. By combining linear and graph genome analysis, they identified over 100,000 sequence-resolved structural variants and genotyped 300,000 multi-allelic tandem repeats across all samples.

The key finding: many structural variants that short-read callers classified as rare were found at substantial population frequencies when examined with long reads. This is especially true in repetitive regions and segmental duplications — areas where short reads fundamentally cannot resolve complex variation. The open-access dataset provides a critical resource for understanding the true scope of human genetic diversity.

Read the paper:

Structural variation in 1,019 diverse humans based on long-read sequencing - Nature Intermediate-coverage long-read sequencing in 1,019 diverse humans from the 1000 Genomes Project, representing 26 populations, enables the generation of comprehensive population-scale structural variant catalogues comprising common and rare alleles.

A common gut microbe in lab mice finally has its genome mapped.

Tritrichomonas musculus is a commensal protist found in many mouse colonies, but its impact on experimental data has been hard to assess without a reference genome. Now, a team led by Alves-Ferreira and Grigg has sequenced and assembled its 193 Mb genome.

For this project, the authors used whole-genome sequencing and RNA-seq services provided by CD Genomics. The assembly revealed a highly repetitive structure and lineage-specific gene expansions that may influence host-microbe interactions.

Read the paper:

Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice - Scientific Data Tritrichomonas musculus is a commensal protist colonizing the large intestine of laboratory mice. Parasite colonization reshapes the gut microbiome and modulates mucosal immunity. This parasite is refractory to axenic culture. In order to facilitate functional genomic investigations we assembled a 1...