Camille Marchet

Extracting and Updating Compact Colored k-mer Indexes

This paper introduces efficient methods to update colored k-mer indexes without rebuilding them from scratch, enabling dynamic maintenance of large genomic collections.

spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

Minimizer Density revisited: Models and Multiminimizers

This paper revisits the concept of density in k-mer-based sequence analysis, introduces multiminimizers as a novel technique, and proposes deduplicated density as a new metric.

Fast Set Operations for Compact k-mer Sets

The paper introduces efficient set operations for SBWT-encoded k-mer spectra, enabling memory-efficient processing of large genomic datasets.

KaryoScope: rapid, alignment-free sequence annotation for the pangenome era

KaryoScope annotates genome assemblies at base-pair resolution across multiple feature classes quickly and without alignment, revealing structural variation in centromeres and subtelomeres.

Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research

Metappuccino uses a fine-tuned large language model to enrich metadata from RNA-seq datasets, improving accuracy and consistency for cancer research.

Helicase: Vectorized parsing and bitpacking of genomic sequences

Helicase provides a fast, vectorized parser for FASTA/Q files, outperforming existing libraries by leveraging SIMD and efficient bitpacking.

Hierarchical genomic feature annotation with variable-length queries

The paper introduces HKS, a method for exact hierarchical k-mer annotation with variable-length queries, achieving high concordance in human genome assemblies.

REINDEER2: practical abundance index at scale

REINDEER2 provides a scalable, dynamic abundance index for RNA datasets, achieving faster construction and accurate abundance recovery.

The Vizitig pangenome and pantranscriptome explorer

Vizitig is a platform for real-time exploration of DNA and RNA de Bruijn graphs across samples, enabling efficient querying and analysis of pangenomic and pantranscriptomic data.

Assessing Long-Read Mappers for Viral Genomics

This study evaluates eight long-read mapping tools for viral genomic data, finding that most struggle with read edges and performance decreases with default settings.

Constrained enumeration of k-mers from a collection of references with metadata

The paper introduces a framework to efficiently enumerate k-mers from a collection of references based on metadata constraints, using a specialized data structure and demonstrating it on microbial and RNA-seq data.

Cdbgtricks: strategies to update a compacted de bruijn graph

Cdbgtricks improves the efficiency of updating compacted de Bruijn graphs by indexing them for fast k-mer location and subgraph queries.

KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction

KaMRaT reduces the dimensionality of k-mer count matrices from high-throughput sequencing data to identify condition-specific sequences.

Exploring a large cancer cell line RNA-sequencing dataset with k-mers

The paper introduces a k-mer-based method to quantify RNA sequences from large RNA-seq datasets, demonstrating its accuracy for variant RNA detection in cancer cell lines.

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets

The paper introduces CBL, a dynamic and exact k-mer set representation that outperforms existing methods and supports in-place set operations.

Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching

This paper introduces a new sketching method for genomic data that reduces space and memory usage while maintaining efficiency and accuracy compared to existing tools.

Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

The paper introduces PAC, a scalable approximate membership query data structure for large sequence collections, achieving faster construction and query times than existing methods.

A survey of mapping algorithms in the long-reads era

This paper surveys long-read mapping algorithms, highlighting their evolution from seed-and-extend to seed-and-chain frameworks and introduces a visualization tool for parameter settings.

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.

BLight: Efficient exact associative structure for k-mers

BLight is a memory-efficient data structure for associating unique identifiers with k-mers and querying them at high speed.

CONSENT: Scalable long read self-correction and assembly polishing with multiple sequence alignment

CONSENT corrects long reads using multiple sequence alignment and de Bruijn graphs, outperforming existing methods on Oxford Nanopore data and enabling efficient processing of ultra-long reads.

Data structures based on k-mers for querying large collections of sequencing datasets

The paper surveys computational methods for indexing and querying large sequencing datasets using k-mer-based data structures.

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

REINDEER indexes k-mer presence and abundance across large sequencing datasets efficiently, processing 2,585 human RNA-seq experiments in 45 hours with 56 GB RAM.

ELECTOR: Evaluator for long reads correction methods

ELECTOR evaluates long reads correction methods by providing efficient and comprehensive metrics to assess quality improvements.

Read correction for non-uniform coverages

This paper introduces BCT, a tool that improves read correction for non-uniform coverage data by cleaning De Bruijn graphs and local alignment, preserving rare variants and improving accuracy in RNA-seq and metagenomic datasets.

Comparative assessment of long-read error-correction software applied to RNA-sequencing data

This paper benchmarks long-read error-correction tools on RNA-sequencing data, finding they improve base-pair accuracy but affect gene family sizes and isoform diversity.

Clustering de Novo by Gene of Long Reads from Transcriptomics Data

This paper introduces a de novo clustering algorithm for long-read transcriptomics data, showing improved performance for Oxford Nanopore reads and non-model species.

A de novo approach to disentangle partner identity and function in holobiont systems

The paper introduces a method to separate host and symbiont reads in holobiont transcriptomes, improving assembly quality and enabling functional analysis.

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

This study compares mapping-first and assembly-first approaches for annotating and differentially analyzing alternative splicing from RNAseq data, showing complementary strengths and advocating their combined use.