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23 results for “HiFi”
Supporting data: HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt
<p>Repository for supporting data to the paper: HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt</p>
PacBio HiFi de-novo assembled genome and mitochondrial genome for Orbicella faveolata
<p>Final assembly using Funannotate of <i>Orbicella faveolata</i> from PacBio HiFi reads. For full methods please see the publication. </p>
Supplemental Results for Assembly, Annotation, and Analysis from HiFi reads of Gulf Toadfish Genome and Transcriptome fOpsBet2.1
<p>This repository contains gzipped tarballs of the results of the various assembly, annotation, and analysis steps performed during the assembly of the fOpsBet2.1 genome assembly for Opsanus beta at the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science for the McDonald Toadfish Lab. These results are too numerous to include as supplemental data for a journal publication and so are available here for review. In this repository you will find results for:</p><p>Scripts:</p><p>-all bash and LSF scheduler job scripts used as part of the analysis, both exploratory and final. </p><p>QC:</p><p>-GenomeScope2 estimation of genome metrics from HiFi Reads</p><p>-QUAST genome statistics for each assembly step</p><p>-BUSCO completeness assessments for each assembly step </p><p>-inspector logs for polishing of initial assembly</p><p>-logs from Kraken2 contaminant screen</p><p>Assembly and Scaffolding:</p><p>-ntLINKS logs and intermediates for initial scaffolding</p><p>-ragtag logs and metrics for super-scaffolding to the ThaAma1.1 T. amazonica reference assembly</p><p>-mitoHIFI results for mitogenome assembly from HiFi reads, primary assembly, and purged alternate assembly</p><p>Annotation:</p><p>-PASA directory with full input and output for SQLite PASA assembly of transcriptome for gene predictors</p><p>-Results folder for Funannotate::annotate for gene models, annotations, and CDS/mRNA/protein fastas</p><p>-InterProSCan5 results for protein annotation used as input into Funannotate</p><p>-ghostKOALA KEGG assignment results for predicted proteins from funannotate results</p><p>Repetitive Elements:</p><p>-tidk telomere repeat analysis results</p><p>-TRAH satellite DNA analysis with subsequent analysis with HiCAT and StainedGlass</p><p>-RepeatModeler results for de novo TE prediction</p><p>-repclassifier results for TE curation</p><p>Comparative Analysis:</p><p>-OrthoFinder ortholog search for O. beta to several other vertebrates</p><p>-CAFE5 gene family expansion and contraction of Orthogroups from OrthoFinder results</p><p> </p>
Test datasets for the IWC workflow Assembly-Hifi-only-VGP3
<p>Test datasets for the workflow Assembly-Hifi-only-VGP3</p> <p>Datasets : </p> <ul> <li>Hifi reads</li> <li>Meryl database</li> <li>Genomescope profile summary</li> </ul> <p> </p>
The HIFI reads and assembled contigs used to construct the mitochondrial genome assembly of Glyphodes pyloalis
<p><span>Glyphodes pyloalis (Lepidoptera; Crambidae; Spilomelinae), known as the mulberry pyralid, is a notorious insect pest belonging to the Lepidopteran that threatens mulberry cultivation across China. <span>The mitochondrial genome is an invaluable genetic resource owing to its maternal inheritance, rapid evolution, and lack of recombination. A previous study documented the G. pyloalis mitochondrial genome (mtDNA) as NC_025933 using short-read next-generation sequences that, while pioneering, leaves room for improvement with modern long-read sequencing. PacBio’s high-fidelity circular consensus sequencing (HIFI CCS) generates extra-long sequences sufficient to produce complete mtDNA assemblies with base pair accuracy.</span></span></p>
A hifi testing dataset derived from SRR13128014 (zymo D6331)
<p>This is a small dataset subsampled from SRR13128014 which represents a mock community, zymoBIOMICS D6331.</p> <p> </p> <p>We extraced E.coli reads by alignment, then used `seqtk subseq read.fq.gz 0.1` to randomly pick 10% from them. This is created for testing if hifiasm-meta (https://github.com/xfengnefx/hifiasm-meta ) runs. For r57, it roughly needs 170s on 48 threads with peak memory of 18GB. Refer to the tar.gz file for expected results. Hicanu and metaflye should be able to successfully run on this dataset as well.</p>
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota.
<p>We reported 102 complete metagenome assembled genomes (cMAGs) from five human fecal HiFi sequencing samples.</p> <p>102_cMAGs_fna.tar.gz: Fasta sequence files of 102 cMAGs.</p> <p>gc_skew_figures.tar.gz: GC-skew pattern figures of 102 cMAGs. (SVG format)</p> <p>coverage_plots.tar.gz: Genome coverage plot of 102 cMAGs.</p>
Control panel created from 30-40 Nanopore or PacBio HiFi sequencing data from the Human Pangenome Reference Consortium
<p>This is control panel for <a href="https://github.com/friend1ws/nanomonsv">nanomonsv</a> software, which is expected to exclude many false positives as well as improve computational cost. This is made by aligning 30-40 Nanopore or PacBio HiFi sequencing data from Human Pangenome Reference Consortium (HPRC) to the GRCh38 or CHM13 reference genomes with <a href="https://github.com/lh3/minimap2">minimap2</a> version 2.24.</p> <p><strong>When you use these control panels and publish, do not forget to credit to <a href="https://humanpangenome.org/data-use-protocol/">HPRC</a>!</strong></p> <div> <div> <div> <p>Reference genomes:</p> <ul> <li>GRCh38: <a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz">Download GRCh38</a></li> <li>CHM13: <a href="https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0_maskedY_rCRS.fa.gz">Download CHM13</a> <div> <div> <div> <div> </div> </div> </div> </div> </li> </ul> </div> </div> </div>
Phased VCF outputs for "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing"
<p>The collection of raw and processed VCF files for the paper titled: "HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing".</p><p>Raw VCF files from DeepVariant, pbsv, and TRGT are included in the unphased subfolder. Outputs from WhatsHap and HiPhase are in their own subfolders. Three replicates of HG002 are included in all subfolders. Layout is as follows:</p><blockquote><p>hiphase_vcfs</p><p>├── all_vcfs.md5</p><p>├── hiphase</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.hiphase.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.hiphase.vcf.gz.tbi</p><p>├── unphased</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep1.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz</p><p>│ ├── HG002-rep2.GRCh38.trgt.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.deepvariant.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz</p><p>│ ├── HG002-rep3.GRCh38.pbsv.vcf.gz.tbi</p><p>│ ├── HG002-rep3.GRCh38.trgt.vcf.gz</p><p>│ └── HG002-rep3.GRCh38.trgt.vcf.gz.tbi</p><p>└── whatshap</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep1.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz</p><p> ├── HG002-rep2.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p> ├── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz</p><p> └── HG002-rep3.GRCh38.deepvariant.whatshap.vcf.gz.tbi</p><p>3 directories, 43 files</p></blockquote>
Identification of a novel non-coding deletion in Allan-Herndon-Dudley syndrome by long-read HiFi genome sequencing
<p>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.</p> <p>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>'.</p>
A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei) - Pacbio HIFI reads
<p>The critically endangered mountain gorilla Gorilla beringei beringei faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7) and 0% switch errors detected. These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.</p> <p>This read set is comprised of fastqs from Pacbio HIFI (3 runs).</p> <p>A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258</p>
WGS of E. coli K12 with PacBio HiFi
<p>WGS of E. coli K12 with PacBio HiFi reads for genome assembly.</p>
Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"
<p>This dataset contains supporting files referenced by the following publication:</p> <p>• Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. <strong>Pushing the limits of HiFi assemblies reveals centromere diversity between two <em>Arabidopsis thaliana</em> genomes</strong>. <em>Nucleic Acids Research</em>. doi: 10.1093/nar/gkac1115</p> <p> </p> <p>Directory structure:</p> <ul> <li><strong>Bionano_optical_maps_based_assemblies</strong>: this directory contains results from the Bionano optical map based scaffolding for the main long-read assemblers analysed in the study for <em>Arabidopsis thaliana</em> accession Ey15-2 (9994): <ul> <li><strong>9994.CLR_Canu</strong></li> <li><strong>9994.HiFi_FALCON</strong></li> <li><strong>9994.HiFi_HiCanu</strong></li> <li><strong>9994.HiFi_Hifiasm</strong></li> <li><strong>9994.HiFi_IPA</strong></li> <li><strong>9994.HiFi_Peregrine</strong></li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Col-0_HiFi-Hifiasm_assembly</strong>: this directory contains the Pacbio HiFi based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Col-0 (6909). </li> </ul> <p> </p> <ul> <li><strong>Ey15-2_HiFi-Hifiasm_plus_CLR-Canu_assembly</strong>: this directory contains the Pacbio HiFi+CLR based chromosome level assembly (fasta file) and repeat annotation (gff file) of <em>Arabidopsis thaliana</em> accession Ey15-2 (9994). </li> </ul> <p> </p> <ul> <li><strong>Naish2021_Wang2021_repeat_annotation</strong>: this directory contains the repeat annotation (gff files) for the <em>Arabidopsis thaliana</em> Col-0 (6909) assemblies performed by Naish <em>et al.</em> (doi: 10.1126/science.abi7489) and Wang <em>et al.</em> (doi: 10.1016/j.gpb.2021.08.003). </li> </ul> <p> </p> <ul> <li><strong>TAIR10_masked</strong>: this directory contains the repeat-hard-masked version of the TAIR10 <em>Arabidopsis thaliana</em> Col-0 (6909) reference genome that was used for in silico scaffolding of contigs with RagTag (<a href="http://github.com/malonge/RagTag">https://github.com/malonge/RagTag</a>).</li> </ul> <p> </p>
High Five (HiFi) Accelerated Partial Breast Irradiation Study
ClinicalTrials.gov study NCT05142202. IPD Sharing: Not stated. Countries: 1. Publications: 52.
dbgphmm KIR+hifi assembly
<p>10x.fa: HiFi reads of HG002 KIR region</p><p>dbgphmm.gfa, hifiasm.gfa, LJA.gfa: obtained assembly graphs</p>
Metagenomic Std ATCC MSA-1003: PacBio HiFi Reads FASTQ
<p>WGS of mock metagenomic community ATCC MSA-1003 using PacBio HiFi (CCS) Sequencing</p>
Haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model
<p>Example dataset for DipPAV</p>
supplemental files for Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio HiFi technologies
<p><span>Supplemental files for Assembly and analysis of sequence from a spring and winter type <em>Camelina sativa</em> by whole genome PacBio HiFi technologies</span></p>
PacBio HiFi based haplotype-aware assemblies of tomato hybrid varieties Funtelle and Maxeza
<p>Modern commercial varieties of tomato (<em>Solanum lycopersicum</em>) are typically F1 hybrids that are genetically heterozygous. Here we generated haplotype-aware assemblies of two different tomato commercial hybrids (Funtelle and Maxeza) using PacBio HiFi reads. The HiFi data was assembled using the Hifiasm assembler allowing for the generation of contigs that distinguish the two parental haplotypes (haplotype-aware assembly). Reference based scaffolding was used to generate the chromosome-scale assemblies available here. It should be noted that although the raw assembly manages to fully distinguish haplotypes we did not test whether the working reference sequence we make available here is fully phased at the chromosome level.</p>
High Frequency Ventilation in Premature Infants (HIFI)
ClinicalTrials.gov study NCT00000567. IPD Sharing: Not stated. Countries: 0. Publications: 2.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.