Genomics and Phylogenetic Studies

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

vardictcpp: A C++ reimplementation of VarDict variant caller

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

A Sense of Direction: Detecting Natural Selection Across Non-Stationary Genomes

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

Accurate ab initio gene prediction in eukaryotes with Tiberius in multiple clades

Extended Tiberius models outscore Helixer and ANNEVO on all 33 genomes from the five clades all three tools cover, and approach BRAKER3 accuracy in four clades without extrinsic evidence.

A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics

A sparse mixture-of-experts DNA model conditioned on hyperbolic taxonomy embeddings learns better microbial representations than its taxonomy-free twin and comes close to Evo2-7B in probing and fine-tuning at lower compute.

kamino: fast proteome-wide variant calling for amino acid phylogenomics

Proteome-wide variant calling builds amino acid phylogenomic alignments orders of magnitude faster than a BUSCO marker pipeline, with similar tree signal in three of four test taxa.

STAR Suite: Transcriptomics processing in a single binary through AI-assisted development

Open-source STAR binary for five transcriptomic assays runs 3.9- to 6.2-fold faster than Cell Ranger 9.0.1 for scRNA-seq and Perturb-seq, 17- to 41-fold for Flex, with closely concordant counts.

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

MAT-classifier: A memory-efficient pipeline for accurate genus level profiling from ancient metagenomic data

Per-genus Bowtie2 or BWA-aln alignments in place of MALT cut alignment-stage memory from about 140 GB (aMeta) to about 7 GB and gave higher simulated-data AUC (0.87 vs 0.79).

A pangenome-graph approach for mapping and imputing barley sequences

Pan20, a Practical Haplotype Graph of 20 barley genomes, assigns sequences MorexV3 coordinates and imputes genotyping-by-sequencing (GBS) reads at 0.06% base-call error versus 0.32% for variant calling.

Omega-seq: ultra-low-background RNA sequencing with faithful molecular counting and precise transcript-end capture

USER-excisable uracil TSOs, a uracil-intolerant polymerase and excess primer confine UMI incorporation to reverse transcription, minimizing background and UMI inflation; a separate Omega-shaped dT primer captures stranded transcript ends.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Evo 2's Perception of Single Nucleotide Substitutions in the Genes of Two Plant Model Organisms

Evo 2 7B assigns higher perplexity to plant gene alleles carrying randomly simulated single-nucleotide substitutions than to those observed in vivo, in Arabidopsis and rice; significant but small effect.

Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2

A ProtT5-embedding, ConvNext-plus-attention ensemble predicts human pathogenic capacity from whole bacterial genomes, outperforming prior predictors on species absent from training and flagging influential proteins.

Helixer--de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model

Helixer, a hybrid convolutional/bLSTM network with a hidden Markov model post-processor, predicts eukaryotic primary gene models from DNA alone, outscoring GenemarkES and AUGUSTUS on most species.

Metalog: curated and harmonised contextual data for global metagenomics samples

Metalog manually curates and harmonises contextual metadata for 110,733 metagenomic samples from humans, animals, ocean water and other environments, linked to taxonomic profiles and SPIRE genomes.

tMHG-Finder: Tree-guided Maximal Homologous Group Finder for Bacterial Genomes

tMHG-Finder uses Mash guide trees and consensus representative sequences to find maximal homologous groups in bacterial genomes with linear scaling, reaching F-score 0.932 on simulated data.

Oatk: a de novo assembly tool for complex plant organelle genomes

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

A contextualised protein language model reveals the functional syntax of bacterial evolution

Trained on over 1.3 million bacterial genomes represented as ordered protein sequences, the transformer foundation model Bacformer predicts protein interactions, operons, essentiality, and phenotypes while generating trait-conditioned synthetic proteomes.

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

OrthoFinder v3 splits orthogroups at duplications predating the species-tree root, raising OrthoBench accuracy, and assigns extra species to a core run, finishing 1024 species in 128 hours.

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing

MEGA12 adds filtered substitution-model selection, matching full-search choices in all 240 simulated nucleotide alignments, and adaptive bootstrapping with an 81% average speed-up, accelerating maximum-likelihood phylogenetics.

Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Rapid and sensitive detection of genome contamination at scale with FCS-GX

FCS-GX, a hashed k-mer cross-species aligner with a 709 Gbp curated database, screens most genomes in 0.1-10 minutes and flagged 36.8 Gbp of contamination in GenBank.