Rayan Chikhi

Strainberry uses long-read data to separate microbial strains in low-complexity metagenomes, achieving high accuracy and additional genomic material in real datasets.

This paper introduces a new method for DNA sequence analysis using minimizer-space de Bruijn graphs, achieving faster and more memory-efficient genome and metagenome assembly with high accuracy.

The paper introduces a method to identify sample-specific strings in long-read sequencing data for comparative genome analysis without read mapping.

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

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

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.

The paper introduces two tools, yacrd and fpa, to improve long-read genome assembly by removing chimeric reads and filtering spurious overlaps, resulting in higher-quality assemblies and faster processing.

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.

The paper introduces an improved Sequence Bloom Tree data structure that enhances query performance for RNA-seq databases.

This paper introduces DE-kupl, a k-mer-based method to capture RNA variation without a reference, identifying novel transcripts and biological events from RNA-seq data.

RecoverY improves Y-chromosome assembly by automatically selecting Y-specific reads using k-mer abundance analysis, outperforming manual methods in simulated and real data.

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

This paper reviews computational pan-genomics, discussing its status, potential, and challenges across multiple biological disciplines.

The paper improves genome scaffolding by addressing PE-contamination in mate-pair libraries using an ILP-based approach in the BESST scaffolder, showing significant quality improvements.