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27 results for “PacBio sequencing”
HiPR-FISH PacBio Sequencing Data
<p>This dataset contains raw fastq files from PacBio sequencing for HiPR-FISH experiments.</p>
SMRT PacBio Sequel sequencing of 12 Silene herbarium specimens
<p>The folder includes reads sequenced with SMRT PacBio Sequel from twelve Silene herbarium specimens. Both demultiplexed and non demultiplexed reads are included. The demultiplexed reads are in folder called "demultiplexed.zip", in files starting with "Barcodenumber_speciesnamesamplingyear.fastq". The barcode number and sequence can be found below, in the description. The non demultiplexed reads are in file called "ps_248_001.ccsreads.fastq.gz".</p> <p>#NebNext Barcodes<br> #Adapter('Barcode 1 (forward)',<br> # start_sequence=('BC01', 'CGTGAT'),<br> # end_sequence=('BC01_rev', 'ATCACG')),<br> #Adapter('Barcode 2 (forward)',<br> # start_sequence=('BC02', 'ACATCG'),<br> # end_sequence=('BC02_rev', 'CGATGT')),<br> #Adapter('Barcode 3 (forward)',<br> # start_sequence=('BC03', 'GCCTAA'),<br> # end_sequence=('BC03_rev', 'TTAGGC')),<br> #Adapter('Barcode 4 (forward)',<br> # start_sequence=('BC04', 'TGGTCA'),<br> # end_sequence=('BC04_rev', 'TGACCA')),<br> #Adapter('Barcode 5 (forward)',<br> # start_sequence=('BC05', 'CACTGT'),<br> # end_sequence=('BC05_rev', 'ACAGTG')),<br> #Adapter('Barcode 6 (forward)',<br> # start_sequence=('BC06', 'ATTGGC'),<br> # end_sequence=('BC06_rev', 'GCCAAT')),<br> #Adapter('Barcode 7 (forward)',<br> # start_sequence=('BC07', 'GATCTG'),<br> # end_sequence=('BC07_rev', 'CAGATC')),<br> #Adapter('Barcode 8 (forward)',<br> # start_sequence=('BC08', 'TCAAGT'),<br> # end_sequence=('BC08_rev', 'ACTTGA')),<br> #Adapter('Barcode 9 (forward)',<br> # start_sequence=('BC09', 'CTGATC'),<br> # end_sequence=('BC09_rev', 'GATCAG')),<br> #Adapter('Barcode 10 (forward)',<br> # start_sequence=('BC10', 'AAGCTA'),<br> # end_sequence=('BC10_rev', 'TAGCTT')),<br> #Adapter('Barcode 11 (forward)',<br> # start_sequence=('BC11', 'GTAGCC'),<br> # end_sequence=('BC11_rev', 'GGCTAC')),<br> #Adapter('Barcode 12 (forward)',<br> # start_sequence=('BC12', 'TACAAG'),<br> # end_sequence=('BC12_rev', 'CTTGTA')),]</p> <p> </p>
Comparing bacterial microbiome composition of Xylocopa species across populations using PacBio 16S rRNA gene sequencing
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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>
Combined high-depth Illumina+PacBio Sequencing of several samples from FDA-ARGOS
<p>The (real) sequencing data is compiled from a concatenation of sequencing runs from Database for Reference Grade Microbial Sequences (FDA-ARGOS). Specifically, the following samples were sequenced with both Illumina and PacBio. The sample accessions are shown below.</p> <pre><code> BioSample Run Platform Organism bases source <chr> <chr> <chr> <chr> <dbl> <chr> 1 SAMN06173354 SRR5409204 ILLUMINA Bacillus anthracis 1778000000 Colorado Serum Co., Anthrax Spore Vaccine 2 SAMN06173354 SRR5409205 PACBIO_SMRT Bacillus anthracis 2420000000 Colorado Serum Co., Anthrax Spore Vaccine 3 SAMN06173356 SRR5448657 ILLUMINA Bacillus circulans 2311000000 swab with brown-gray powder 4 SAMN06173356 SRR5448656 PACBIO_SMRT Bacillus circulans 242000000 swab with brown-gray powder 5 SAMN04875535 SRR4123920 ILLUMINA Elizabethkingia anophelis 1357000000 blood 6 SAMN04875535 SRR4123919 PACBIO_SMRT Elizabethkingia anophelis 2173000000 blood 7 SAMN06173306 SRR5413253 ILLUMINA Escherichia coli O157 3051000000 clinical isolate 8 SAMN06173306 SRR5413252 PACBIO_SMRT Escherichia coli O157 915000000 clinical isolate 9 SAMN06173318 SRR5413272 ILLUMINA Mycobacterium avium subsp. paratuberculosis 1032000000 feces 10 SAMN06173318 SRR5413271 PACBIO_SMRT Mycobacterium avium subsp. paratuberculosis 462000000 feces 11 SAMN07312468 SRR5879398 ILLUMINA Mycobacterium tuberculosis 1054000000 human 12 SAMN07312468 SRR5879396 PACBIO_SMRT Mycobacterium tuberculosis 1854000000 human 13 SAMN04875542 SRR4123931 ILLUMINA Neisseria gonorrhoeae 1053000000 ATCC strain 14 SAMN04875542 SRR4123930 PACBIO_SMRT Neisseria gonorrhoeae 1117000000 ATCC strain </code></pre> <p>Samples were selected with the SRA Run selector. The SraRunTable.txt file was exported containing the metadata for each sample, and fastq-dump from the SRA toolkit was used to write out fastq files for each run, with paired Illumina data being split into separate _1.fastq.gz and _2.fastq.gz files. </p>
IsoQuant graphs from PacBio and ONT Mouse sequencing data
<p>Graph files and simulated ONT BAM files.</p>
Pacbio single molecule sequencing
<p>As a leading genomics company, CD Genomics provides next-generation sequencing and bioinformatics services to pharmaceutical and biotech companies, as well as academic and government agencies around the world, relying on advanced sequencing instruments and rich project experience. We are offering long-read sequencing services from PacBio and Oxford Nanopore, giving researchers a wide range of cutting-edge sequencing services to suit the particular needs of any project. Here, we offer long-read sequencing services which are based on <a href="https://longseq.cd-genomics.com/pacbio-smrt-sequencing-technology.html">PacBio single molecule sequencing</a> technology, the Sequel II System. This technology can produce highly accurate (> 99.9% average concordance accuracy) long sequences up to 30 kb long, helping to identify biologically important structural variants, RNA splice site isoforms of cDNA, and provide insights into hard-to-sequence regions of the genome, among others.</p>
PacBio whole-genome sequencing and draft assembly of Stentor coeruleus
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PacBio sequencing output increased through uniform and directional 5-fold concatenation
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Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups. This sample includes most currently recognized Botrychium species in Europe and North America, and the majority of our specimens were genotyped with co-dominant nuclear allozymes to ensure species identification. We analyzed the sequence data using maximum likelihood (ML) and Bayesian inference (BI) concatenated-data ("gene tree") approaches to explore the relationships among Botrychium species. Finally, we estimated divergence times among Botrychium lineages and inferred the multi-labeled polyploid species tree showing the origins of the polyploid taxa, and their relationships to each other and to their diploid progenitors. We found strong support for the monophyly of the major lineages within Botrychium and identified most of the parental donors of the polyploids; these results largely corroborate earlier morphological and allozyme-based investigations. Each polyploid had at least two distinct homeologs, indicating that all sampled polyploids are likely allopolyploids (rather than autopolyploids). Our divergence-time analyses revealed that these allopolyploid lineages originated recently—within the last two million years—and thus that the genus has undergone a recent radiation, correlated with multiple independent allopolyploidizations across the phylogeny. Also, we found strong parental biases in the formation of allopolyploids, with individual diploid species participating multiple times as either the maternal or paternal donor (but not both). Finally, we discuss the role of polyploidy in the evolutionary history of Botrychium and the interspecific reproductive barriers possibly involved in these parental biases.
Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions
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NBS-LRR PacBio sequencing from a Glycine max diversity panel
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PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci – processed datasets
<p>Processed datasets from PacBio amplicon re-sequencing of 62 P. tricornutum genomic loci. Raw data are available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA658511. </p> <p>Available datasets: </p> <p>- reference file for regions selected for amplicon sequencing: <em>Phaeodactylum_tricornutum_amplicon_sequencing_loci.fa</em></p> <p>- final .bam files containing processed PacBio sequencing reads aligned to the reference:</p> <p><em>PacBio_amplicon_seq_T1.bam</em> and <em>PacBio_amplicon_seq_T6.bam</em> </p> <p>- . table files with the position, reference and alternative allele for reliable biallelic SNPs selected in ILLUMINA sequencing of the culture at T1: </p> <p><em>P_tricornutum_PacBio_amplicon_sequencing_T1_SNPs.table</em> and <em>P_tricornutum_PacBio_amplicon_sequencing_T6_SNPs.table</em></p> <p>Re-sequencing of 62 endogenous P. tricornutum loci selected in a genome-wide analysis of haplotype diversity. The goal was to determine the number of haplotypes per locus and the appearance of new haplotypes over time. The length of the sequenced loci was 2kb (+/- 5%). Loci were amplified by emulsion PCR on the same culture harvested in two time points: five loci were amplified one month (T1) and all loci were amplified 6 months (T6) after the start of the culture from a single cell. Plasmids containing cloned GFP or YFP were amplified separately as a control for random errors. Control reactions for artificial haplotypes detection consisted of mixed CFP with YFP or CFP with GFP. Amplicons were pooled together into two samples. Sample PacBio_AS_T1 contained five P. tricornutum endogenous amplicons from DNA harvested at T1 time point, GFP amplified separately and CFP+YFP amplified in one reaction. Sample PacBio_AS_T6 contained 63 P. tricornutum endogenous amplicons from DNA harvested at T6 time point, YFP amplified separately and CFP+GFP amplified in one reaction. Samples were mixed in 1:9 PacBio_AS_T1: PacBio_AS_T6 ratio before sequencing on one PacBio Sequel SMRT cell.</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>
Supplementary material 1 from: Gueidan C, Elix JA, McCarthy PM, Roux C, Mallen-Cooper M, Kantvilas G (2019) PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens. MycoKeys 53: 73-91. https://doi.org/10.3897/mycokeys.53.34761
: Data type: measurement
PacBio sequencing E. coli doi: 10.1099/mgen.0.000352
<p>PacBio sequencing E. coli doi: 10.1099/mgen.0.000352</p>
Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
Difficulties in generating nuclear data for polyploids have impeded phylogenetic study of these groups. We describe a high-throughput protocol and an associated bioinformatics pipeline (PURC: "Pipeline for Untangling Reticulate Complexes") that is able to generate these data quickly and conveniently, and demonstrate its efficacy on accessions from the fern family Cystopteridaceae. We conclude with a demonstration of the downstream utility of these data by inferring a multilabeled species tree for a subset of our accessions. We amplified four ~1kb-long nuclear loci and sequenced them in a parallel-tagged amplicon sequencing approach using the PacBio platform. PURC infers the final sequences from the raw reads via an iterative approach that corrects PCR and sequencing errors and removes PCR-mediated recombinant sequences (chimeras). We generated data for all gene copies (homeologs, paralogs, and segregating alleles) present in each of three sets of 50 mostly-polyploid accessions, for four loci, in three PacBio runs (one run per set). From the raw sequencing reads PURC was able to accurately infer the underlying sequences. This approach makes it easy and economical to study the phylogenetics of polyploids, and in conjunction with recent analytical advances, facilitates investigation of broad patterns of polyploid evolution.
Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing
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PacBio sequencing of Cp/Wp-driven transcripts from B95-8 LCLs
GEO Series GSE102102. Homo sapiens. 2 samples. Type: Other.
Methylome of Salmonella enterica subsp. Enterica serovar Javiana str. CFSAN001992 by PacBio SMRT Sequencing
GEO Series GSE45178. Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992. 1 samples. Type: Methylation profiling by high throughput sequencing.
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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.