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nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

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

Quadrupling the protein family space with global metagenomics

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

metagRoot: A comprehensive database of protein families associated with plant root microbiomes

metagRoot provides a database of 71,091 enriched protein families from plant root microbiomes, annotated with structural and functional information to aid in microbiome research.

GenomeFace: a deep learning-based metagenome binner trained on 43,000 microbial genomes

GenomeFace improves metagenomic binning by combining composition and environmental abundance networks, producing more near-complete genomes faster than existing methods.

Critical Assessment of Metagenome Interpretation - the second round of challenges

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Profiles of expressed mutations in single cells reveal subclonal expansion patterns and therapeutic impact of intratumor heterogeneity

Trisicell infers subclonal expansion patterns and therapeutic impact of intratumor heterogeneity from scRNAseq data, revealing correlations between mutational composition and tumor aggressiveness.

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

BELLA improves long-read sequencing overlap detection and assembly by balancing precision and recall, achieving high F1 scores on real and synthetic data.

GPU accelerated partial order multiple sequencealignment for long reads self-correction

The paper introduces a GPU-accelerated partial order alignment method for improving the efficiency of long read error correction in sequencing technologies.