Anton Korobeynikov

Petabase-scale Papillomavirus Discovery

The paper searches a petabase-scale dataset to discover new Papillomaviruses, identifying 383 novel types across 105 host species and highlighting biodiversity hotspots.

Blackbird: structural variant detection using synthetic and low-coverage long-reads

Blackbird improves structural variant detection using synthetic and low-coverage long-reads, achieving comparable performance to high-coverage tools with less data.

SpLitteR: Diploid genome assembly using linked TELL-Seq reads and assembly graphs

SpLitteR improves diploid genome assembly using linked TELL-Seq reads and assembly graphs, achieving higher contiguity without additional misassemblies.

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.

Benchmarking state-of-the-art approaches for norovirus genome assembly in metagenome sample

The paper benchmarks state-of-the-art viral assembly tools on norovirus metagenome samples, showing they can assemble samples into single contigs without additional preprocessing.

wastewaterSPAdes: SARS-CoV-2 strain deconvolution using SPAdes toolkit

This paper introduces wastewaterSPAdes, an assembly-based method for SARS-CoV-2 strain deconvolution from wastewater samples without read alignment, showing accurate strain identification and abundance estimation.

BinSPreader: refine binning results for fuller MAG reconstruction

This paper introduces a tool to refine binning results in metagenomic assemblies, improving MAG completeness without reducing purity and predicting contigs belonging to multiple MAGs.

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.

Petabase-scale sequence alignment catalyses viral discovery

The paper develops a cloud computing infrastructure for petabase-scale sequence alignment, identifying over 105 novel RNA viruses and expanding known species by an order of magnitude.

coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies

coronaSPAdes improves RNA viral genome assembly, particularly for coronaviruses, by leveraging viral genome structure knowledge.

SPAligner: alignment of long diverged molecular sequences to assembly graphs

SPAligner aligns long diverged molecular sequences to assembly graphs, efficiently mapping third-generation sequencing data and aiding gene identification in metagenomics.

PathRacer: racing profile HMM paths on assembly graph

PathRacer aligns profile HMMs directly to assembly graphs to recover sequences of interest from fragmented metagenome assemblies.

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

MetaRiPPquest identifies RiPPs by combining genome/metagenome mining with mass spectrometry analysis, discovering 5 novel natural products from 6 datasets.