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opencc-by-4.0Feb 2022View details →

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

Imaging data related to the "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures" manuscript

opencc-by-4.0Feb 2023View details →

MinION plasmid deep long read sequencing for sequence verification

We sequenced four plasmid constructs, each with a whole MinION flowcell, for use in developing and testing a sequence verification procedure. The resulting pipeline can sequence verify plasmid constructs, generating a consensus sequence with associated confidence of each base, adhering to strict acceptance criteria . The data contained herein are a subset of the complete data; 30 fast5 files for each plasmid, to be used as example data.   datHL_001519: BCRxV.TF.1 datHL_001521: BCRxV.VSVG.1 datHL_001617: BCRxV.GagPolRev.1 datHL_001620: BCRxV.VSVG.1_mutant

opencc-by-4.0Apr 2023View details →

Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)

Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing. This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.

opencc-zeroMay 2023View details →

Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing

Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium Halotia branconii CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of generating complete quality genome sequences of microorganisms isolated from extreme intertidal environments, facilitating in-depth evaluation of ecological and taxonomic inferences.

opencc-by-4.0Oct 2023View details →

HG002 data for Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

This dataset includes 6mA frequency data for the HG002 native DNA (untreated) sample sequenced on nanopore r9.4.1.

opencc-by-4.0Oct 2023View details →

NA12878 and MCF7 data for Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing

This dataset includes 5mC and 6mA frequency data for NA12878 and MCF7 EcoGII-treated chromatin samples sequenced on nanopore r9.4.1.

publicApr 2022View details →

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

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publicSep 2022View details →

Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

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publicJul 2022View details →

Long-read-based draft genome sequence of Indian black gram IPU-94-1 ‘Uttara’: Insights into disease resistance and seed storage protein genes

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publicMay 2023View details →

Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing

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opencc-by-4.0Apr 2020View details →

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

The data presented in "NanoGalaxy: A Galaxy tool kit with workflows for third-generation sequence analysis" to illustrate the functionality of the tools was obtained from: Wick, Ryan R., et al. "Completing bacterial genome assemblies with multiplex MinION sequencing." Microbial genomics 3.10 (2017). + Li, Ruichao, et al. "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data." Gigascience 7.3 (2018): gix132.

opencc-zeroJan 2021View details →

Improved contiguity of the threespine stickleback genome using long-read sequencing

While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76% of the gaps in the existing reference genome assembly, improving contiguity over five-fold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

opencc-by-4.0Apr 2024View details →

Identification of a novel non-coding deletion in Allan-Herndon-Dudley syndrome by long-read HiFi genome sequencing

These are the VCF files of structural variant (SV) calls for two sibling patients (II:2 [GMPB009_1] and II:3 [GMPB009_4]) generated by PacBio HiFi long-read genome sequencing. Sequence reads were processed using the <a href="https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake">PacBio Human WGS workflow</a> with the human reference genome (hg38), and SVs were identified using '<a href="https://github.com/PacificBiosciences/svpack">svpack</a>'.

opencc-zeroDec 2021View details →

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Cloning agronomically important genes from large, complex crop genomes remains challenging. Here, we generate a 14.7-gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping, and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance against the devastating fungal stripe rust disease. We identified the race-specific disease resistance gene Yr27, encoding an intracellular immune receptor, as a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13, with the Yr27 and Lr13 proteins sharing 97% sequence identity. Our results thus demonstrate the feasibility of generating chromosome-scale wheat assemblies to clone genes and also exemplify that highly similar alleles of a single-copy gene can confer resistance to different pathogens, which might provide a basis for engineering Yr27 alleles with multiple recognition specificities in future.

opencc-by-4.0Oct 2022View details →

Methods for structural variant detection with long-read sequencing data

SV calls from different long-read based SV callers on sequencing data. SV results evaluated in Methods for structural variant detection with long-read sequencing data. NA24385_Pacbio_HiFi -> HiFi_L1 in paper NA24385_Pacbio_MtSinai -> CLR_L1 in paper NA24385_Pacbio_CLR_SRX7668835 -> CLR_L2 in paper NA24385_Pacbio_CLR_SRX6719924 -> CLR_L3 in paper NA24385_ONT_Promethion -> Nano_L1 in paper

opencc-zeroOct 2022View details →

Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main ABO allele groups: ABO*A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire ABO gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per ABO group were re-sequenced using Illumina and PacBio technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered four genetic variants putatively specific for ABO*A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

opencc-by-4.0Feb 2018View details →

Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"

Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.

opencc-by-4.0Aug 2024View details →

Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals

We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.

opencc-zeroAug 2021View details →

Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing

Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating EGFR mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the EGFR exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five EGFR haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.