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68 results for “Pangenomics”
Data and code pertaining to the pangenome of E coli (2024)
<p>This contains all Jupyter notebooks used to download, filter, enrich, curate, and analyze the pangenome of E coli (2024). It also contains important tables of interest (metadata of strains used in this study, as well as the L matrix (NMF), the A matrix (NMF) and gene annotation table (from eggNOG-mapper-v5) ).</p> <p> </p> <p>bioRxiv to Manuscript for citation is here: https://doi.org/10.1101/2024.06.07.598014</p>
Data for: Pangenome evaluation of gene essentiality in Streptococcus pyogenes
<p>This is the raw output files of analyses using methods within the <a href="https://transit.readthedocs.io/en/latest/">Transit</a> toolkit on <em>Streptococcus pyogenes</em> transposons sequencing datasets. In total there are nine datasets of both Tn5-like and Himar1-like transposons.</p> <p>Information about read handling and analysis of the data can be found in the publication: https://doi.org/10.1101/2023.08.29.555273 </p>
Pangenome-based Genome Inference
<p>Haplotype-resolved assemblies ("haplotype-resolved-assemblies.tar.gz"), the variant callset and pangenome graph ("callset-and.graph.tar.gz") produced from these assemblies, callsets and graphs used for the "leave-one-out" evaluation ("leave-one-out.tar.gz"), and PanGenie genotypes ("cohort-genotypes.tar.gz") for 300 samples (consisting of 100 trios) selected from the 1000 Genome samples.</p> <p><strong>Abstract:</strong></p> <p>Typical analysis workflows map reads to a reference genome in order to genotype genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden.<br> In contrast, recent k-mer based genotypers are fast, but struggle in repetitive or duplicated genomic regions.<br> We propose a novel algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference in conjunction with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation - a process we refer to as <em>genome inference</em>.<br> Compared to mapping-based approaches, PanGenie is more than 4x faster at 30x coverage and reaches significantly better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (>=50bp) and variants in repetitive regions, enabling the inclusion of these classes of variants in genome-wide association studies. PanGenie efficiently leverages the increasing amount of haplotype-resolved assemblies to unravel the functional impact of previously inaccessible variants while being scalable to thousands of genotyped samples.</p>
Chromosome communities in the human pangenome
<p>Results of the analysis of the acrocentric chromosome community in the human pangenome. The plots were presented at the T2T/HPRC assembly meeting on May 9th, 2022.</p>
Data for "Haplotype-aware pantranscriptome analyses using spliced pangenome graphs"
<p>This archive contains mapping benchmark tables and haplotype-specific expression estimates from the paper "Haplotype-aware pantranscriptome analyses using spliced pangenome graphs".</p> <p> </p>
From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula
<p><strong>Introduction:</strong> In <em>Eragrostis curvula</em>, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant.</p> <p><strong>Methods:</strong> To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first <em>E. curvula</em> pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software.</p> <p><strong>Results:</strong> The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior.</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>
PangeBlocks: customized construction of pangenome graphs via maximal blocks
<p>All data regarding experiments presented in the main manuscript and supplementary material. </p> <ul> <li>msas created with MAFFT</li> <li>pangenome graphs created with VG, PGGB and pangeblocks</li> <li>list of sequences and sequences ID used to create the MSAs (SARS-CoV-2 from ENA)</li> <li>pangeblocks experiments: scalability (RAM and User Time) and variation graphs creation for each MSA </li> </ul> <p> </p>
Pangenome of pigs
<p>This dataset contained the annotation file of three different breeds, including Laiwu, Meishan and, Tongcheng pigs. The SNPs and SVs in 18 pig assembilies can be accessed by this dataset. The graph-based pangenome was constructed using vg combined with Sscrofa11.1 reference genome and the SVs in the 18 pig assemblies. SNPs and SVs detected in the 599 pig genomes are also updated in this dataset.</p>
Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew
<p>Data produced for the comparison of six <em>Peronospora effusa</em> isolates. For each isolate, we provide the genome assemblies, gene and repeat annotation, effector clustering, and gene variation. Additionally, we provide the repeat library that was used to annotate the transposable elements for each isolate and the pangenome graph.</p> <p>DOI: https://doi.org/10.1101/2024.05.30.596583 </p>
Arab Pangenome Reference
<p>Pangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phased <em>de novo</em> assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.</p>
Solanaceae pangenome annotations
<p>Datasets produced in the Resistify Solanaceae pangenome project.</p> <p>gene_annotation: gff files of gene coordinates predicted by Helixer</p> <p>te_annotation: transposable element annotations produced by EDTA</p> <p>resistify_output: resistify results for each genome</p> <p>peptide: peptide sequences for each annotated gene</p> <p>N0.tsv: orthofinder orthogroup datasheet</p>
The SV information of A02 and the genotype information based on super-pangenome
<p>A02.SV.vcf is the SV information between the A02 genome and Nipponbare genome.</p> <p>238rice.all.bamSV.vcf is the raw data of the SV genotyping information based on the super pan-genome.</p> <p> </p>
Functional profiling and evolutionary analysis of a marine microalgal virus pangenome
<p>Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, <em>Coccolithovirus</em>, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the <em>Coccolithovirus</em> pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early expression based on a transcriptomic dataset of <em>Coccolithovirus</em> EhV-201 algal infection, were more likely to be similar to host proteins than the non-core set, and were more likely to be involved in vital functions such as replication, recombination, and repair. In addition, we generated and collated annotations for the EhV representative EhV-86 from 12 different annotation sources, building up information for 142 previously hypothetical and putative membrane proteins. AlphaFold was further able to predict structures for 204 EhV-86 proteins with a modelling accuracy of good–high. These functional clues, combined with generated AlphaFold structures, provide a foundational framework for the future characterization of this model genus (and other giant viruses) and a further look into the evolution of the <em>Coccolithovirus</em> proteome.</p>
Potato super pangenome v1.0
<p><span class="ui-provider km b c d e f g h i j k l m n o p q r s t u v w x y z ab ac ae af ag ah ai aj ak">Potato (<em>Solanum sp</em>., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the <em>Solanum</em> section <em>Petota</em>, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of <em>Solanum</em> section <em>Petota</em> composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The <em>Petota</em> core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for <em>Solanum</em> section <em>Petota</em>.</span></p>
Genomic Answers for Kids pangenome graph and allele definitions
<p>This publication contains the Genomic Answer for Kids genome graph, the observes alleles and their frequencies.</p> <p>Included is a short document describing how to generate the graph, genotype samples, merge genotypes and identify singleton SVs.</p> <p>Related information such as assembly contig sizes, assembly intervals validated with Flagger, sequencing depth and repeat masking results are also included.</p> <p>Miscellaneous scripts that process and generate some of this data is also included.</p> <p>However, the assemblies and the genotypes, of each assembly, or any combination of identifying information cannot be included.</p>
Zymoseptoria tritici pangenome resources
<p>This repository is a collection of reference-quality genomes available for the fungal wheat pathogen Zymoseptoria tritici.</p>
Potato super pangenome v1.0
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Functional profiling and evolutionary analysis of a marine microalgal virus pangenome
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Fitness consequences of structural variation inferred from a House Finch pangenome
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.