Genomics and Phylogenetic Studies

EGGS generates empirical genotype data with missing values by replicating genotype distributions across segments, offering tools for data manipulation and format conversion.

OMAnnotator improves genome annotation by integrating multiple evidence sources using evolutionary information, outperforming existing pipelines in re-annotating Drosophila and other genomes.

ViralClust reduces large viral sequence datasets by clustering, preserving genetic diversity and reducing computational burden.

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

agtools provides a Python framework to manipulate assembly graphs across formats, enabling analysis and integration into bioinformatics workflows.

The paper introduces UMImap, a pipeline for accurate UMI identification and error correction in nanopore sequencing, enabling reliable full-length transcriptome analysis and discovery of novel isoforms.

This study benchmarks genome annotation tools using Nanopore dRNA data from a non-model crop plant, finding significant variation in performance and identifying novel transcripts.

MADRe improves strain-level metagenomic classification by combining assembly-driven database reduction with probabilistic read mapping, achieving higher precision and fewer false positives than existing tools.

The paper introduces annoSnake, a Snakemake workflow for taxonomic and functional annotation of metagenomes and MAGs, providing a scalable and reproducible solution for microbiome analysis.

The paper introduces PlasBin-HMF, a method for plasmid binning from short-read assemblies, which outperforms existing methods by preserving explainability.

MicroFinder improves bird genome curation by identifying conserved microchromosome genes to anchor manual assembly of fragmented microchromosomes.

Pipeasm automates large chromosome-scale genome assembly using HiFi, ONT, and HiC data, enabling diploid genome assembly with a Snakemake pipeline.

PG-SCUnK evaluates pangenome graph representativeness by analyzing single-copy and universal k-mers from source assemblies.

This paper uses trio-binning to assemble the Cannabis genome, revealing structural variation and defining paralog cohorts with high resolution.

The paper introduces ntSynt, a tool for detecting multi-genome synteny blocks using minimizer graphs, showing high coverage and efficiency across diverse genomes.

MMonitor provides real-time analysis and visualization of metagenomic data, enabling dynamic microbiome research through automated pipelines and interactive dashboards.

This study produces high-quality genome assemblies for two Neotropical bumblebee species using long-read sequencing.

Clair3-RNA is a deep learning variant caller for long-read RNA sequencing data that achieves high accuracy in SNP detection across different platforms.

The paper presents chromosome-level genome assemblies of four Diamesa species, revealing gene family contractions and expansions linked to cold tolerance and high-altitude adaptations.

The paper presents a chromosome-level genome assembly for the rare lava gull using Oxford Nanopore sequencing, providing a resource for phylogeography and population genetics studies.

This paper shows that using larger gene families with multiple copies can reduce long-branch attraction errors in phylogenetic analysis, improving accuracy compared to single-copy genes.

The paper identifies a single Indian bekang strain with a conserved accessory gene profile similar to the Japanese natto clade, suggesting a shared adaptive strategy despite phylogenetic divergence.

RNAcentral integrates literature and gene-level data to enhance non-coding RNA sequence analysis and functional understanding.

The paper introduces PhyloSketch, an app for visualizing and improving the layout of phylogenetic trees and networks, with features for capturing topology from figures and minimizing reticulate edge displacement.

This paper introduces pangenome-informed language models for generating synthetic DNA sequences, showing improved efficiency and quality over classical methods.

The paper presents the first telomere-to-telomere, chromosome-level reference genome for the common five-lined skink, providing a highly complete and annotated genome sequence.

SquiDBase provides a centralized repository for raw nanopore sequencing data from microbes, along with tools to process and expand reference datasets.

The paper introduces an embedding-based scoring method for protein sequence alignment, showing it outperforms BLOSUM matrices and existing tools.