All Stories

  1. VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements
  2. Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
  3. K-mer analysis of long-read alignment pileups for structural variant genotyping
  4. StratoMod: predicting sequencing and variant calling errors with interpretable machine learning
  5. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
  6. STIX: Long-reads based Accurate Structural Variation Annotation at Population Scale
  7. Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair for somatic benchmarks
  8. The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics
  9. MethPhaser: methylation-based long-read haplotype phasing of human genomes
  10. De novo genome assembly for the coppery titi monkey (Plecturocebus cupreus) – an emerging non-human primate model for behavioral research
  11. Unveiling microbial diversity: harnessing long-read sequencing technology
  12. The benefit of a complete reference genome for cancer structural variant analysis
  13. Improved sequence mapping using a complete reference genome and lift-over
  14. Sniffles2 methods v1
  15. Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
  16. VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements
  17. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
  18. MethPhaser: methylation-based haplotype phasing of human genomes
  19. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
  20. Variant calling and benchmarking in an era of complete human genome sequences
  21. Impact and characterization of serial structural variations across humans and great apes
  22. Multiscale Analysis of Pangenome Enables Improved Representation of Genomic Diversity For Repetitive And Clinical Relevant Genes
  23. Fixing reference errors efficiently improves sequencing results
  24. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene
  25. A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
  26. Author Correction: Searching thousands of genomes to classify somatic and novel structural variants using STIX
  27. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms
  28. Improved sequence mapping using a complete reference genome and lift-over
  29. Read2Tree: scalable and accurate phylogenetic trees from raw reads
  30. Searching thousands of genomes to classify somatic and novel structural variants using STIX
  31. A complete reference genome improves analysis of human genetic variation
  32. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
  33. Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity
  34. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device
  35. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus
  36. Hidden biases in germline structural variant detection
  37. Comprehensive analysis of GBA using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing
  38. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells
  39. Author Correction: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
  40. High resolution copy number inference in cancer using short-molecule nanopore sequencing
  41. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation
  42. Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
  43. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
  44. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
  45. Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
  46. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals
  47. A strategy for building and using a human reference pangenome
  48. Fully resolved assembly of Cryptosporidium parvum
  49. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus
  50. Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device
  51. Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes
  52. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment
  53. Towards population-scale long-read sequencing
  54. The complete sequence of a human genome
  55. Author Correction: Discovery and population genomics of structural variation in a songbird genus
  56. Intronic Haplotypes in the GBA Gene Do Not Predict Age at Diagnosis of Parkinson's Disease
  57. Mining Thousands of Genomes to Classify Somatic and Pathogenic Structural Variants
  58. SVhound: Detection of future Structural Variation hotspots
  59. Optimized sample selection for cost-efficient long-read population sequencing
  60. muCNV: genotyping structural variants for population-level sequencing
  61. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
  62. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
  63. High resolution copy number inference in cancer using short-molecule nanopore sequencing
  64. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals
  65. Chromosome-scale, haplotype-resolved assembly of human genomes
  66. Parliament2: Accurate structural variant calling at scale
  67. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
  68. precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
  69. Complex mosaic structural variations in human fetal brains
  70. A diploid assembly-based benchmark for variants in the major histocompatibility complex
  71. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine
  72. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
  73. SVCollector: Optimized sample selection for cost-efficient long-read population sequencing
  74. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals
  75. Benchmarking challenging small variants with linked and long reads
  76. Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
  77. Author Correction: A robust benchmark for detection of germline large deletions and insertions
  78. Discovery and population genomics of structural variation in a songbird genus
  79. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
  80. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
  81. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
  82. A robust benchmark for detection of germline large deletions and insertions
  83. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
  84. Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes
  85. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions
  86. Targeted nanopore sequencing with Cas9-guided adapter ligation
  87. Paragraph: a graph-based structural variant genotyper for short-read sequence data
  88. Structural variant calling: the long and the short of it
  89. Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing
  90. Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION
  91. The population genomics of structural variation in a songbird genus
  92. A Genocentric Approach to Discovery of Mendelian Disorders
  93. RaGOO: fast and accurate reference-guided scaffolding of draft genomes
  94. Accurate chromosome-scale haplotype-resolved assembly of human genomes
  95. A strategy for building and using a human reference pangenome
  96. Evaluation of computational genotyping of structural variation for clinical diagnoses
  97. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
  98. Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
  99. Author Correction: Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
  100. A robust benchmark for germline structural variant detection
  101. Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast
  102. Paragraph: A graph-based structural variant genotyper for short-read sequence data
  103. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato
  104. Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations
  105. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel
  106. A multi-task convolutional deep neural network for variant calling in single molecule sequencing
  107. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2
  108. Evaluation of computational genotyping of Structural Variations for clinical diagnoses.
  109. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase
  110. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
  111. Fast and accurate reference-guided scaffolding of draft genomes
  112. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome: Supplementary Material
  113. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing: Supplemental Figures and Tables
  114. Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish
  115. Atlas-CNV: a validated approach to call Single-Exon CNVs in the eMERGESeq gene panel
  116. Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers
  117. Ancestral admixture and structural mutation define global biodiversity in fission yeast
  118. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
  119. SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants
  120. Accurate detection of complex structural variations using single-molecule sequencing
  121. Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
  122. xAtlas: Scalable small variant calling across heterogeneous next-generation sequencing experiments
  123. Piercing the dark matter: bioinformatics of long-range sequencing and mapping
  124. Detection of GBA missense mutations and other variants using the Oxford Nanopore MinION
  125. Tools for annotation and comparison of structural variation
  126. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
  127. Accurate detection of complex structural variations using single molecule sequencing
  128. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin
  129. DangerTrack: A scoring system to detect difficult-to-assess regions
  130. GenomeScope: fast reference-free genome profiling from short reads
  131. LRSim: a Linked Reads Simulator generating insights for better genome partitioning
  132. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
  133. LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning
  134. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
  135. The genomic basis of circadian and circalunar timing adaptations in a midge
  136. SplitThreader: Exploration and analysis of rearrangements in cancer genomes
  137. Phased diploid genome assembly with single-molecule real-time sequencing
  138. GenomeScope: Fast reference-free genome profiling from short reads
  139. Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
  140. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
  141. Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe.
  142. The pineapple genome and the evolution of CAM photosynthesis
  143. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
  144. The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
  145. Ectodysplasin signalling genes and phenotypic evolution in sculpins ( Cottus )
  146. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data
  147. Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study
  148. ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain
  149. Corrigendum: Updating benchtop sequencing performance comparison
  150. NextGenMap: fast and accurate read mapping in highly polymorphic genomes
  151. Updating benchtop sequencing performance comparison
  152. Benefit-of-doubt (BOD) scoring: A sequencing-based method for SNP candidate assessment from high to medium read number data sets
  153. Advanced Methylome Analysis after Bisulfite Deep Sequencing: An Example in Arabidopsis
  154. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs