Claire Lemaitre

Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

The paper introduces a method to measure differences between pangenome graphs using pairwise graph edit distance and applies it to yeast and human datasets.

Investigating the topological motifs of inversions in pangenome graphs

The paper investigates inversion topological motifs in pangenome graphs and finds significant variation in inversion representation across pipelines, with poor recovery in real human data.

Mapler: Assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads

Mapler evaluates Hi-Fi long read metagenome assemblies, providing metrics to assess quality and identify bottlenecks in genome reconstruction.

The Silene latifolia genome and its giant Y chromosome

This study sequences the giant Y chromosome of Silene latifolia and reveals its structure, function, and evolutionary history.

MTG-Link: leveraging barcode information from linked-reads to assemble specific loci

MTG-Link assembles specific loci from linked-read data by leveraging barcode information, improving local assembly and characterizing large insertion variants.

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.

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

LEVIATHAN is a structural variant caller that improves scalability and applicability across organisms using Linked-Reads data.

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

The paper investigates why short-read variant callers fail to detect many insertions by analyzing callsets from long-read technologies and simulating the impact of insertion features on recall.

MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities

MinYS assembles a specific symbiont genome from metagenomic data, achieving high-quality results even with distant references and diverse samples.

DiscoSnp-RAD: de novo detection of small variants for population genomics

DiscoSnp-RAD efficiently detects small variants in RAD-Seq data, revealing population structure and outperforming existing tools in speed.

SVJedi: Genotyping structural variations with long reads

SVJedi genotypes known structural variants from long read sequencing data with high accuracy, outperforming existing methods for long reads.

Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps

The paper sequenced two ichneumonid wasp genomes to reveal distinct genomic architectures of endogenous ichnoviruses compared to bracoviruses.

DiscoSnp++: de novo detection of small variants from raw unassembled read set(s)

DiscoSnp++ detects SNPs and small indels from raw NGS data without a reference genome, achieving high precision and recall on simulated and real datasets.

Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.