The SeqOccIn Project aims to compare the potential of different front-end sequencing technologies (Illumina, Pacific Biosciences, Oxford Nanopore) and methodologies in three scientific areas: genome assembly and structural variant identification (4263 samples), methylation mark detection (224 samples), and metagenomics (436 samples). Long and short fragment sequencing data were generated for various agronomically important animal and plant species: including cattle, goat, sheep, pig, quail, and corn. In total, more than 4900 samples were sequenced and used in the following applications: i) genome assembly (Long reads, Hi-C and 10x linked reads), ii) punctual and structural variations analyses (including low pass sequencing), iii) methylation mark analyses from both native DNA (Oxford Nanopore) and converted DNA based approaches (EMseq, Bisulfite sequencing), iv) metabarcoding analyses (long read 16S and operon sequencing), and whole genome metagenomics analyses (PacBio HiFi).
Accession | PRJEB60075 |
Type | Umbrella project |
Submission | Registration date: 21-Feb-2023 INRAE - GeT-PlaGe |
Project Data:
Resource Name | Number of Links |
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Sequence data |
Nucleotide (total) | 43 |
WGS master | 13 |
Genomic DNA | 30 |
SRA Experiments | 3698 |
Other datasets |
BioSample | 740 |
Assembly | 13 |
This project encompasses the following 12 sub-projects:
Project Type | Number of Projects |
Genome sequencingHighest level of assembly : Chromosomes Contigs Total | 1 1 2
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BioProject accession | Assembly level | Name | Title |
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PRJEB68295 | Contigs | INRAE Bovine long-read WGS | Whole-genome sequencing of 154 bulls (INRAE - GeT-PlaGe) | PRJEB55064 | Chromosomes | WGS Bos Taurus | Whole-genome sequencing of 2 bovins trio (INRAE - GeT-PlaGe) |
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Other | 10 |
BioProject accession | Name | Title |
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PRJEB68296 | INRAE bovine Graph Genomes | Whole-genome sequencing of cattle trios (INRAE - GeT-PlaGe) | PRJEB59364 | Long-read sequencing affected by interchromosomal rearrangements. | Long-read sequencing of the genomes of normozoospermic artificial insemination bulls affected by interchromosomal rearrangements. (INRAE - GeT-PlaGe) | PRJEB60080 | Shotgun metagenomic data from SeqOccIn project | Shotgun metagenomic data from mock communities and pig faeces samples (INRAE - GeT-PlaGe) | PRJEB60079 | Targeted metagenomic data from SeqOccIn project | Targeted metagenomic data from mock communities and pig faeces samples (INRAE - GeT-PlaGe) | PRJEB64023 | WGS Bos Taurus Males | Whole-genome sequencing of 567 bulls (INRAE - GeT-PlaGe) | List all 10 'Other' projects...BioProject accession | Name | Title |
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PRJEB68296 | INRAE bovine Graph Genomes | Whole-genome sequencing of cattle trios (INRAE - GeT-PlaGe) | PRJEB59364 | Long-read sequencing affected by interchromosomal rearrangements. | Long-read sequencing of the genomes of normozoospermic artificial insemination bulls affected by interchromosomal rearrangements. (INRAE - GeT-PlaGe) | PRJEB60080 | Shotgun metagenomic data from SeqOccIn project | Shotgun metagenomic data from mock communities and pig faeces samples (INRAE - GeT-PlaGe) | PRJEB60079 | Targeted metagenomic data from SeqOccIn project | Targeted metagenomic data from mock communities and pig faeces samples (INRAE - GeT-PlaGe) | PRJEB64023 | WGS Bos Taurus Males | Whole-genome sequencing of 567 bulls (INRAE - GeT-PlaGe) | PRJEB55065 | WGS Coturnix japonica | Methylation calling of a quail from 4 sequencing methods (INRAE - GeT-PlaGe) | PRJEB55066 | WGS Sus scrofa | Methylation calling of a pig from 3 sequencing methods (INRAE - GeT-PlaGe) | PRJEB74075 | WGS of Alpine goat breed | 26 animals were selected to represent French Alpine breed diversity (INRAE - GeT-PlaGe) | PRJEB69684 | WGS of French dairy sheep breed | 62 animals were selected in various herds to represent Basco-Béarnaise, Manech Tête Noire and Corse sheep breed diversity (INRAE - GeT-PlaGe) | PRJEB74076 | WGS of Saanen goat breed | 25 animals were selected to represent French Saanen breed diversity (INRAE - GeT-PlaGe) | Less... |