Arend Sidow

Benchmarking challenging small variants with linked and long reads

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

MARS: a tool for haplotype-resolved population-based structural variation detection

MARS detects haplotype-resolved structural variants from linked-read assemblies using Mendelian inheritance and HiFi reads, achieving 73%-87% validation rates for indels.

De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures

SparseSignatures is a framework for discovering mutational signatures in tumor genomes, outperforming existing methods and identifying signatures linked to known mutagenic mechanisms in pancreatic and breast tumors.

Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads

Aquila uses linked-read data to assemble diploid genomes and detect genetic variants, achieving high coverage and accurate phasing of SNPs, indels, and structural variants.

Aquila_stLFR: diploid genome assembly basedstructural variant calling package for stLFRlinked-read

Aquila_stLFR is a tool for diploid genome assembly and structural variant calling using stLFR linked-read data, achieving high sensitivity for deletions and specificity for insertions.

De novo diploid genome assembly for genome-wide structural variant detection

This study demonstrates that de novo assembly of 10x linked-read data can effectively detect structural variants in personal genomes with high accuracy and cost-effectiveness.

Assessment of human diploid genome assembly with 10x Linked-Reads data

This study evaluates how 10x Linked-Read sequencing parameters affect human genome assembly quality using real and simulated data, finding optimal coverage and fragment length ranges.

Culture-free generation of microbial genomes from human and marine microbiomes

This paper introduces a read cloud metagenomic sequencing approach combined with a new assembler, Athena, to generate high-quality microbial genome drafts from human and marine microbiomes without culturing.

genomeview - an extensible python-based genomics visualization engine

The paper introduces genomeview, a Python-based genomics visualization engine designed for extensibility and integration into analysis pipelines.

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

HAPDeNovo filters and phases de novo mutations in linked read sequencing data to reduce false positives while maintaining sensitivity.

Genome-wide reconstruction of complex structural variants using read clouds

This paper introduces GROC-SVs, a method for detecting and assembling structural variants using read cloud data, showing improved specificity and enabling complex breakpoint reconstruction in cancer samples.

Extensive sequencing of seven human genomes to characterize benchmark reference materials

The paper presents extensive sequencing data from seven human genomes to serve as benchmark reference materials for improving sequencing technologies and variant calling.

svviz: a read viewer for validating structural variants

svviz validates structural variants by visualizing relevant reads aligned to candidate SV alleles, enabling evidence assessment and breakpoint refinement.