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718 results for “illumina”
Illumina CRAM files for "Characterization of large-scale structural variants using Linked-Reads" (Part 1 of 2)
<p>Here we propose novel algorithms to characterize large (>40 Kbp) interspersed segmental duplications, (> 80 Kbp) inversions, (> 100 Kbp) deletions, and (> 100 Kbp) translocations using Linked-Read sequencing data. Linked-Read sequencing provides long range information, where Illumina reads are tagged with barcodes that can be used to assign short reads to pools of larger (30-50 Kbp) molecules.</p> <p><br> Our methods rely on split molecule sequence signature that we have previously described. Similar to the split read, split molecules refer to large segments of DNA that span an SV breakpoint. Therefore, when mapped to the reference genome, the mapping of these segments would be discontinuous.</p> <p><br> We redesign our earlier algorithm, VALOR, to specifically leverage Linked-Read sequencing data to discover large <br> structural variation. We implement our new algorithms in a new software package, called VALOR2. </p>
Illumina reads SARS-Cov-2 using amplicon enrichment
<p>Testing data for <a href="https://github.com/nf-core/viralrecon">nf-core/viralrecon</a> pipeline</p> <p>.Here we share two samples with illumina reads obtained from a enrichment experiment using Artic network amplicons V1 for SARS-Cov-2 virus. We also share the fasta and bed file with the localization of the primers in the virus genome.</p> <p>The library has been constructed performing the next steps:</p> <p>- Amplicon creation.</p> <p>- Illumina library generation. No fragmentation, only adaptor and indexes.</p> <p>- MiSeq 2x300 sequencing.</p> <p> </p>
[BIOCOM-PIPE] Example and expected output files with an Illumina dataset
<p>BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons</p> <p><strong>Summary:</strong></p> <p>This Zenodo repository encompasses the <em>d</em>emo input files and expected output files in the pipeline such that before directly applying it on large-scale datasets, a user can be assured that he/she has successfully implemented the pipeline. More precisely, we chose to use a recent dataset published (Sadet et al., 2018 – Applied Soil Ecology – DOI: 10.1016/j.apsoil.2018.02.006), with raw datasets areavailable in the EBI database system under project accession number PRJEB14258. We hope that these files will help users to efficiently test and checked the BIOCOM-PIPE pipeline. The deposited archive includes :</p> <p>- the Input.txt file with chosen parameters,</p> <p>- the project.csv file describing the composition of the library,</p> <p>- .fastq files from the EBI database system under project accession number PRJEB14258,</p> <p>- the expected result files and summary files after BIOCOM-PIPE analysis.</p> <p> </p> <p><strong>Background:</strong></p> <p>The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. There exists a growing number of metabarcoding pipelines, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool.</p> <p><strong>Results:</strong></p> <p>BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (i) remove chimeras based on read abundance, (ii) align sequences with structure-based alignments of RNA homologs using covariance models or a post-clustering tool (ReClustOR), and (iii) re-assign OTUs based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) highlighted that BIOCOM-PIPE was better at discriminating land use groups.</p> <p><strong>Conclusions:</strong></p> <p>The BIOCOM-PIPE pipeline makes it possible to analyze 16S/18S and 23S rRNA genes in the same package tool. This innovative approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs. For advanced users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily.</p>
Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
Genetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.
Snakemake workflow for Illumina bacterial assembly and QC v1.0.1
<p>This Illumina bacterial assembly snakemake repo is a snakemake workflow to assemble bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification, installation instructions provided in the README). The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/illumina-bacterial-assembly-snakemake and was updated to v1.0.1 with interactive and printer-friendly HTML and PDF reports summarising all QC metrics of reads and assemblies, tool versions used and a graphical workflow overview.</p>
Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex
<p>This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the <i>Valenzuela flavidus </i>(Psocodea: Psocomorpha: Caeciliusidae) Species Complex".</p> <p><i>Valenzuela flavidus</i> is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, <i>Valenzuela aurantiacus</i> was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain North American populations. Cytogenetic studies have demonstrated European all-female populations are triploid. However, males are often reported in North America suggesting diploidy for sexual populations. With the use of Illumina whole genome sequencing, genetic diversity among North American and European populations was explored with phylogenomic methods. Ploidy level was estimated by examining allele frequencies of read-mapped homologous gene regions. Results indicate divergent populations between Europe and North America. North American populations containing males are estimated to be diploid suggesting a different mechanism of genomic reproduction. These results suggest divergent population structure among European asexual and North American sexual members of <i>V. flavidus</i> providing insight for future studies to understand patterns of asexuality reported within the complex.</p> <p>The following file contains all gene alignments, concatenated supermatrix, and mitochondrial alignment for this manuscript. In addition, the BAM files used to estimate allele frequencies. Also, gene trees for coalescent analysis, resultant treefiles from IQ-tree searches, and MCMCtree result.</p>
Hybrid assembly comparisons Illumina reads
<p>Illumina reads for 49 natural isolates of E.coli used in the Hybrid genome assembly comparison study, first isolated by Ishii et al.</p> <p> </p> <p>Ishii, S., W.B. Ksoll, R.E. Hicks, and M.J. Sadowsky. 2006. Presence and Growth of Naturalized Escherichia Coli in Temperate Soils from Lake Superior Watersheds. Applied and Environmental Microbiology 72, no. 1: 612–621 </p>
Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
<p>For any genome-based research, a robust genome assembly is required. <em>De novo</em> assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least three phases: i) short-read only, ii) short- and long-read hybrid, and iii) long-read only assemblies. Each of the phases has their own error model. We hypothesized that hidden scaffolding errors in short-read assembly and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of <em>T. borchgrevinki</em> from data generated during each of the three phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-mer-based strategy improved short-read assemblies as measured by BUSCO while mate-pair libraries introduced hidden scaffolding errors and perturbed BUSCO scores. Further, we found that although hybrid assemblies can generate higher contiguity, they tend to suffer from lower quality. In addition, we found long-read-only assemblies can be optimized for contiguity by sub-sampling length-restricted raw reads. Our results indicate that long-read contig assembly is the current best choice and that assemblies from phase I and phase II were of lower quality.</p>
Sequence and assembly artifacts: GRCr8 and Illumina reads from BN
<p>GRCr8 rat reference genome assembly polishing data.</p>
Benchmarking Illumina RNA-seq fusion transcript detection methods - simulated 101 base PE reads
<p>Simulated 101 base paired-end reads used for benchmarking Illumina-based fusion detection methods as used in:</p> <p>Haas, B.J., Dobin, A., Li, B. <em>et al.</em> Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. <em>Genome Biol</em> <strong>20</strong>, 213 (2019). https://doi.org/10.1186/s13059-019-1842-9</p> <p> </p>
SARA module 3: NGS epitope sequencing: Illumina FASTQ files
<p>We investigate the accumulated microbial and autoantigen antibody repertoire in adult-onset dermatomyositis patients sero-positive for TIF1γ (TRIM33) autoantibodies. We use an untargeted high-throughput approach which combines immunoglobulin disease-specific epitope-enrichment and identification of microbial and human antigens. We observe antibodies recognizing a wider repertoire of microbial antigens in dermatomyositis. Antibodies recognizing viruses and Poxviridae family species are significantly enriched. The identified autoantibodies recognise a large portion of the human proteome, including interferon regulated proteins; these proteins cluster in specific biological processes. In addition to TRIM33, we identify autoantibodies against eleven further TRIM proteins, including TRIM21. Some of these TRIM proteins share epitope homology with specific viral species including poxviruses. Our data suggest antibody accumulation in dermatomyositis against an expanded diversity of microbial and human proteins and evidence of non-random targeting of specific signalling pathways. Our findings indicate that molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.</p>
16S Illumina Sequencing of Aguamiel Microbiota
<p>Dataset of the 16S gene V4 region Illumina Sequencing of <em>Agave salmiana </em>sieve's (aguamiel) microbial community.</p>
The ILLUMINA Study. (ILLUMINA)
ClinicalTrials.gov study NCT03510676. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Data from: A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing
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Data from: Development and characterization of thirty-three microsatellite markers for the Patagonian sprat, Sprattus fuegensis (Jenyns, 1842), using paired-end Illumina shotgun sequencing
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Data from: Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing
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LNCRNA Illumina sequencing results associated with renal fibrosis disease progression
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Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki
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SARA module 3: NGS epitope sequencing: Illumina FASTQ files
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Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform
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