Genomics and Phylogenetic Studies

skani estimates average nucleotide identity (ANI) from sparse FracMinHash k-mer chains, staying robust to incomplete, fragmented metagenome-assembled genomes while running over 20 times faster than FastANI.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

NextDenovo corrects noisy Nanopore reads faster and more accurately than Canu and Necat; its maize and 35 human-genome assemblies are more contiguous, with fewer misassemblies, than Flye's.

YaHS, a C command-line Hi-C scaffolder, normalises inter-contig contacts by intra-contig medians, yielding more contiguous, accurate chromosome-scale scaffolds than SALSA2 and pin_hic.

MuRaL, a two-module neural network using only DNA sequence, estimates nucleotide-level germline substitution rates, outperforming k-mer and feature-based human models at fine regional scales.

Marker genes for 26,970 species-level genome bins, 4,992 defined only by metagenome-assembled genomes, let MetaPhlAn 4 quantify uncharacterized species and beat MetaPhlAn 3, mOTUs and Bracken on synthetic benchmarks.

Gfastats, a C++ tool, computes genome assembly statistics in linear time, converts between FASTA, FASTQ and GFA files, and edits assemblies through a bidirected graph.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

Bakta annotates bacterial genomes with one taxon-independent database, uses MD5-hash protein lookups to skip alignments and assign cross-references, detects small proteins, and lowers hypothetical-protein rates versus Prokka/DFAST.

Rebuilt on eggNOG v5, eggNOG-mapper v2 raises average annotation rate by 608% over v1 and adds Prodigal gene calling, pairwise ortholog reports, and PFAM/SMART domain prediction.

A C++ library plus 83 command line utilities and 44 scripts (vcflib) for filtering, transforming and computing population-genetic statistics on VCF files, with companion tools bio-vcf, slivar, cyvcf2 and hts-nim.

Dual patterned unique molecular identifiers (UMIs) turn Nanopore or PacBio CCS reads of ~4400 bp rRNA operons into single-molecule consensus sequences with 0.0049% (ONT) or 0.0006% (PacBio) mean error.

One R function runs discrete-trait ancestral state reconstruction in MrBayes 3.2.7a on a fixed tree, returning per-node state probabilities and a pie-chart tree plot from plain-text inputs.

clinker aligns translated genes from GenBank gene clusters, orders clusters by homology-plus-synteny similarity, and renders interactive, editable comparison figures via the D3-based clustermap.js library.

gEVAL-assisted manual curation of 111 VGP and DToL assemblies averaged 221 interventions per Gb, raising mean scaffold N50 by 40% and cutting scaffold counts by 29%.

Merqury estimates assembly consensus quality, k-mer completeness, and trio-based phasing from read k-mers alone, avoiding reference alignment; validated on Arabidopsis F1 hybrid and human NA12878 assemblies.

Exhaustive gapped short-read aligner BURST returns all optimal matches above an identity cutoff, with tie-breaking or LCA taxonomy, at 1,000,000 reads/minute against 5,500 prokaryotic genomes (32 cores).

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

Stand-alone, point-and-click Java toolkit bundling over 100 sequence, BLAST, GO/KEGG enrichment and interactive plotting functions, so wet-lab biologists can analyse sequencing-scale data without the command line.

IQ-TREE 2 implements taxon-coverage-aware gene concordance factors and introduces site concordance factors, quantifying gene- and site-level discordance that 100% bootstrap support leaves hidden.

TALON annotates and counts full-length reads from PacBio or Nanopore in one framework; in mouse brain, 422 genes showed more novel-isoform reads than annotated ones.

PICRUSt2 places 16S rRNA variants into a 20,000-gene reference tree, predicting gene families, pathways and phenotypes; gene-family predictions matched or beat four tools against shotgun metagenomes.

BlobToolKit combines GC proportion, read coverage and taxonomic hits per contig in an interactive browser Viewer, exposing contaminants and cobionts across public eukaryotic genome assemblies.

Hybrid polisher that leaves solid-k-mer-supported contig regions untouched gave HG002 long-read assemblies fewer errors than Racon in under one-third the time and about half the memory.

Mutect2 calls somatic SNVs and indels via local haplotype assembly, Bayesian genotyping and F-score-optimised filtering, with roughly one false call per 5 Mb in exome replicate-versus-replicate tests.

StringTie2 assembles error-prone long reads, recovering on average 8.3 and 2.6 times as many correct transcripts as FLAIR and Traphlor, and outperforms Scallop on short reads.

Kraken 2's minimizer-keyed compact hash table cuts memory 85% versus Kraken 1 and classifies over 5 times faster with comparable accuracy; translated search boosts viral sensitivity.

OrthoFinder now infers orthogroups, rooted gene and species trees, duplications and orthologs from proteomes alone, topping Quest for Orthologs accuracy tests while rivaling heuristic tools' speed.

Permutation-based maximal matched-pairs symmetry tests show 40.8% of 3,572 partitions from 35 published phylogenetic datasets reject stationary, reversible, homogeneous evolution, frequently altering inferred tree topologies.