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525 results for “Long reads”
A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing
<p>This is a public repository containing secondary datasets described in the publication <a href="https://doi.org/10.26508/lsa.202302481">"A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing"</a>. Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets:</p> <p>REH cell line:</p> <ul> <li>PacBio WGS</li> <li>ONT Ultralong WGS</li> <li>Illumina short-read PCR-free WGS</li> <li>IsoSeq RNA-seq</li> <li>Illumina short-read RNA-seq</li> </ul> <p>GM12878 cell line:</p> <ul> <li>Illumina short-read RNA-seq</li> </ul> <p>This dataset includes the following files:</p> <p><strong>Depth of Coverage analysis</strong></p> <ul> <li>Output from `samtools coverage`: <em>samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt</em></li> <li>Output from `copycat` (binned coverage): <em>copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv</em></li> </ul> <p><strong>Structural Variant (SV) callsets</strong></p> <ul> <li><strong>Raw:</strong> <em>illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf</em></li> <li><strong>Filtered: </strong><em>REH.svs.filtered.csv</em></li> </ul> <p><strong>SNV callsets</strong></p> <ul> <li><strong>Filtered and annotated:</strong> <em>REH.mutect.filtered.ann.vcf.gz</em></li> </ul> <p><strong>Fusion gene callsets</strong></p> <ul> <li><strong>Short-read: </strong><em>GM12878.fusionreport.txt, illumina.all.txt, illumina.filtered.csv, REH.arriba.fusions.tsv, REH.fusioncatcher.fusion-genes.txt, REH.pizzly.txt, REH.squid.fusions.annotated.txt, REH.starfusion.abridged.tsv, REH.pdf</em></li> <li><strong>Long-read: </strong><em>cupcake.long.csv, cupcake.std.csv, jaffa_results.csv</em></li> <li><strong>Filtered: </strong><em>REH.fusions.filtered.csv</em><br> </li> </ul> <p> </p>
Resolution, validation and divergence of heterozygous haplotypes from pooled long read sequencing of the diamondback moth (Lepidoptera: Plutellidae)
<p>This data sets includes the full set of intermediate genome assemblies produced during our analyses. We make these available for researchers who may be interested in the variation between assembly results and variation within the study organism (<em>Plutella xylostella</em>) prior to removal during subsequent genome processing.</p>
A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13
<p>PacBio Sequence data associated with genetic stock KDH13.Datasets include genome resources and annotated files associated with the manuscript "Long-read genome assembly of Double Haploid Sugar Beet KDH13 provides roadmap for durable genetic resistance to Beet Curly Top Virus". This includes genome assembly, ordered genome assembly, protein predictions, variant call format files for an F1 hybrid (KDH13xKDH19-17).</p>
Tspe_v1 (Telopea speciosissima) genome supplementary files for: Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C
<p><i>Telopea speciosissima, </i>the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for <i>T. speciosissima</i>. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs 'Complete'. We present a new method in Diploidocus (<a href="https://github.com/slimsuite/diploidocus">https://github.com/slimsuite/diploidocus</a>) for classifying, curating and QC-filtering scaffolds, which combines read depths, <i>k</i>-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (<a href="https://github.com/slimsuite/depthsizer">https://github.com/slimsuite/depthsizer</a>), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2<i>n</i> = 22). Genome annotation predicted 40,158<code> </code>protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated <i>CYCLOIDEA </i>(<i>CYC</i>)<i> </i>genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 'Duplicated' BUSCO genes using a new tool, DepthKopy (<a href="https://github.com/slimsuite/depthkopy">https://github.com/slimsuite/depthkopy</a>), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level <i>T. speciosissima</i> reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.</p>
Long-read DNA-Seq of SmAP1 knockout strains
<p>Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 μg/mL) complex medium (CM) until mid-exponential phase (OD600nm = 0.5). The cultures were grown at 37C, under light exposure, and with constant agitation (125 RPM). We collected 2 mL samples and submitted them to DNA extraction using the DNeasy Blood & Tissue kit (QIAGEN), according to the manufacturer's instructions for Gram-negative bacteria. We tested DNA samples for purity and quantity using spectrophotometric and fluorimetric methods, respectively. The samples were prepared for long-read sequencing following the 1D native barcoding genomic DNA protocol using SQK-LSK108 and EXP-NBD103 (Oxford Nanopore Technologies). The equimolar pool of barcoded samples was sequenced using a MinION Mk1B instrument (Oxford Nanopore Technologies) in an FLO-MIN106 flow cell for 24 hours. Three biological replicates were sequenced for each one of the strains (control and SmAP1 knockout). This repository stores the partitioned (eleven parts: aa-ak) compressed directory (tar.gz) containing all the raw reads (fast5 format) output by the MinKNOW software.</p> <p><strong>Experimental design:</strong></p> <table> <tbody> <tr> <td><strong>Barcode</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>Barcode 01</td> <td>Control, biological replicate 1</td> </tr> <tr> <td>Barcode 02</td> <td>Control, biological replicate 2</td> </tr> <tr> <td>Barcode 03</td> <td>Control, biological replicate 3</td> </tr> <tr> <td>Barcode 04</td> <td>SmAP1 knockout, biological replicate 1</td> </tr> <tr> <td>Barcode 05</td> <td>SmAP1 knockout, biological replicate 2</td> </tr> <tr> <td>Barcode 06</td> <td>SmAP1 knockout, biological replicate 3</td> </tr> </tbody> </table> <p><strong>Instructions to merge files and extract:</strong></p> <p>1. Download all the files available in this Zenodo entry (smap1_ko_exp_fast5.tar.gz.part_a*; from aa to ak; eleven files) to your preferred directory;</p> <p>2. Execute the following commands using a Linux or OSX terminal:</p> <pre><code class="language-bash"># concatenate all the files into a single one cat smap1_ko_exp_fast5.tar.gz.part_a* > smap1_ko_exp_fast5.tar.gz # extract the merged file tar zxvf smap1_ko_exp_fast5.tar.gz</code></pre> <p> </p>
Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
<p>Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generate the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ~70,000 extant vertebrate species.</p>
Long-read-based draft genome sequence of Indian black gram IPU-94-1 'Uttara': Insights into disease resistance and seed storage protein genes
<p>Black gram [Vigna mungo (L.) Hepper var. <em>mung<a>o</a></em>] [LAV1] is a warm-season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high-quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, 'Uttara' (IPU 94-1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single-molecule real-time (SMRT) and Illumina sequencing assembled a draft reference-guided assembly with a cumulative size of ~454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high-quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single-copy ortholog [BUSCO] score 94.17%), and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein-coding genes, from which, ~95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site–leucine rich repeat (NBS-LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs.</p>
Genome-resolved metagenomics using short-, long-read and metaHiC sequencing
<p>Reference-quality metagenome-assembled genomes (MAGs) are the key to exploring microbial compositions and microbe-phenotype associations. They can be recovered by different sequencing technologies and computational tools, which need an unbiased and comprehensive assessment to identify best practices. This work systematically evaluates 40 distinct strategies to recover high-quality MAGs generated by eight assemblers, eight metagenomics binners, and four sequencing technologies, including short-, long-read and metaHiC sequencing. We notice that the hybrid assemblies of short- and long-reads outperform either short- or long-read assemblies and generate more contigs with high contiguity. When the hybrid assemblies are combined with metaHiC-based binning (Hybrid-HiC), more high-quality MAGs with higher taxonomic diversity are recovered, and more tRNA and rRNA genes, phages, plasmids and antibiotic resistance genes are identified in the mock, simulated and real datasets.</p>
Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
<p><span>Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. </span>RNA-Bloom2 is available on GitHub at: <a href="https://github.com/bcgsc/RNA-Bloom">https://github.com/bcgsc/RNA-Bloom</a>.</p> <p><span>We benchmarked the assembly quality and the computational performance of RNA-Bloom2 on simulated data. We prepared two mouse simulated datasets with Trans-NanoSim</span><span> for the cDNA and dRNA sequencing protocols model on experimental ONT data</span><span>. The datasets were simulated </span><span>based on the mouse ENSEMBL annotation for GRCm39.</span><span> To investigate the effect of sequencing depth, we subsampled each dataset to 2, 10, and 18 million reads, resulting in a total of six sets of reads for our benchmarking experiments. Using the simulated data, w</span><span>e showed that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods.</span></p>
Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing - Real and mock datasets
<p>This repository contains the reads, assemblies, and references required to replicate the <strong>real and mock</strong> results presented in the paper: https://doi.org/10.1101/2023.01.31.526521</p>
Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing - Simulated datasets
<p>This repository contains the reads, assemblies, and references required to replicate the <strong>simulated</strong> results presented in the paper: https://doi.org/10.1101/2023.01.31.526521</p>
Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing
<p>Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has significant advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the cohort. We identified 20 distinct pathogenic variants, including <span>three</span> novel small variants and <span>five</span> <span>somatic</span> SVs. Furthermore, our analysis shows that the vast majority (93.8%) of <em>RB1</em>-disrupted patients fit the two-hit hypothesis through diverse types, including the biallelic hypermethylated promoter as well as small and large compound heterozygous mutations which were missing in SRS analysis. By constructing the evolutionary history of all genetic variants, we reveal the evolution trends that <em>RB1</em> disruption early and followed by copy number changes, including amplifications of Chr2p, and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data. <br><br>We took IGV screenshots of SV and SNV/indels. The IGV naming conventions for SV is: sample name, chromosome 1, start, chromosome 2, end, SV type, SV length, SV breakpoint. The IGV naming convention for SNV/indels is: sample name, chromosome, position, reference allele, alternate allele.</p>
SPAligner: alignment of long error-prone reads to assembly graphs
<p>This repository contains benchmarking datasets and scripts for the manuscript "SPAligner: alignment of long error-prone reads to assembly graphs". </p> <p>Graph representation of genome assemblies has been recently used in different applications — from gene finding to haplotype separation. While many of these applications are based on aligning DNA and protein sequences to assembly graphs, existing software tools for finding such alignments have important limitations. We present a novel SPAligner (Saint Petersburg Aligner) tool for aligning long reads to assembly graphs and demonstrate that it generates accurate alignments.</p> <p> </p> <p> </p>
Novel canine high-quality metagenome-assembled genomes by long-read metagenomics together with Hi-C proximity ligation
<p>We characterized a canine fecal sample of a healthy dog by combining a long-read metagenomics assembly (Nanopore sequencing) with Hi-C cross-linking data, and further correction of the frameshift errors. We retrieved and characterized 27 HQ MAGs and seven MQ MAGs considering MIMAG criteria.</p> <p>Find in this repository the final Hi-C genomics bins (CanMAG_XX-HiCbin.fa), including both the genome and the extra-chromosomal elements within the bin. </p> <p> </p>
Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
<p>This repository contains annotations for the strains of <em>R. irregularis</em> chromosome assemblies.</p>
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data (repository for simulated ONT RNA-seq data)
<p>Simulated ONT direct RNA and 1D cDNA sequencing data of varying sequencing depths (0.5 million, 1 million, 3 million, and 5 million simulated reads) used for benchmark evaluations of transcript discovery and quantification in our paper "ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data". All details can be found in the <strong>Materials and Methods</strong> section of the paper. </p> <p><em>HEK293T_DirectRNA.transcriptome_quantification.tsv</em> and <em>HEK293T_DirectRNA.transcriptome_quantification.tsv </em>are tab-separated files containing estimated raw read counts and normalized abundance values (in TPM) of transcripts annotated in GENCODE v34lift37. Transcript quantification was done using NanoSim (version 3.1.0). </p> <p><em>HEK293T_DirectRNA.NanoSim_500k.fastq.gz</em>,<em> </em><em>HEK293T_DirectRNA.NanoSim_1M.fastq.gz</em>, <em>HEK293T_DirectRNA.NanoSim_3M.fastq.gz</em>, and<em> HEK293T_DirectRNA.NanoSim_5M.fastq.gz </em>are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT direct RNA sequencing reads respectively. </p> <p><em>HEK293T_1DcDNA.NanoSim_500k.fastq.gz</em>,<em> HEK293T_1DcDNA.NanoSim_1M.fastq.gz</em>, <em>HEK293T_1DcDNA.NanoSim_3M.fastq.gz</em>, and<em> HEK293T_1DcDNA.NanoSim_5M.fastq.gz </em>are gzip compressed FASTQ files containing 0.5 million, 1 million, 3 million, and 5 million simulated ONT 1D cDNA sequencing reads respectively. </p>
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms
<p>Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful but nevertheless produced substantial datasets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (> 515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (> 11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.</p>
Multiplexed long-read plasmid validation and analysis using OnRamp
<p>Plasmid read data and references from "Multiplexed long-read plasmid validation and analysis using OnRamp "</p> <p>Experiments:</p> <ol> <li>AAZ605 - 7 plasmids</li> <li>AFQ178 - 9 plasmids</li> <li>ACK577 - 30 plasmids</li> <li>AEZ576 - 15 plasmids</li> <li>plasmids_ref_7.fasta</li> <li>plasmids_ref_9.fasta</li> <li>plasmids_ref_15.fasta</li> <li>plasmids_ref_30.fasta</li> </ol> <p> </p>
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures
<p>Imaging data related to the "Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures" manuscript</p>
MinION plasmid deep long read sequencing for sequence verification
<p>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.</p> <p> </p> <p>datHL_001519: BCRxV.TF.1<br> datHL_001521: BCRxV.VSVG.1<br> datHL_001617: BCRxV.GagPolRev.1<br> datHL_001620: BCRxV.VSVG.1_mutant</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.