Lithobates pipiens (northern leopard frog), aLitPip1
收藏NIAID Data Ecosystem2026-05-01 收录
官方服务:
资源简介:
This project collects the sequencing data and assemblies generated for Lithobates pipiens/Rana Pipiens (northern leopard frog) by the Canadian BioGenome Project (PRJNA813333) and CanSeq150 Project (PRJNA706690) provided by CGEn, Canada's national platform for genome sequencing and analysis, and its partners. The data under this project are made available subject to the Canadian BioGenome Project Open Data Release Policy.
应用场景:
创建时间:
2023-08-04
相关数据集
Syrphus vitripennis, genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Syrphus vitripennis to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem10
Bicyclus anynana (squinting bush brown), genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Bicyclus anynana, common name squinting bush brown, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem10
Sacculina carcini (crab hacker barnacle), genomic and transcriptomic data. qxSacCarc
This project collects the genomic and transcriptomic data generated for Sacculina carcini, common name crab hacker barnacle, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem20
Cryptosporidium parvum isolate:43IA8 Genome sequencing. Cryptosporidium parvum isolate:43IA8
The objective of this BioProject is to assembly and annotate fully a reference genome for comparative genomics analysis of Cryptosporidium parvum using combined data from PacBio and Illumina sequencing. The existing fully assembled C. parvum reference genome has 10 sequence gaps, which have led to the mis-assembly of the scaffolds. It has also under-estimated the number of genes in the C. parvum genome. A re-assembled and re-annotated reference genome would be useful in the assembly and analysis of C. parvum genomes from field isolates.
NIAID Data Ecosystem10
Paraplatypeza atra, genomic and transcriptomic data. idParAtra
This project collects the genomic and transcriptomic data generated for Paraplatypeza atra to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem00
Complete T2T assembly of the Gila monster (Heloderma suspectum)
Final genome assembly files associated with the first public, complete T2T squamate genome, Gila monster (Heloderma suspectum).Heloderma_suspectum.final.reference.fasta -- Final reference assembly containing the longest autosomes between both haplotypes, the Z and W chromosomes, as well as the mitogenome (i.e. hap1 + chrW + mtDNA). The pseudoautosomal region (PAR) on chrW is soft masked (lowercase). Useful for studies conducting whole-genome alignments, synteny analysis, etc. This is the version submitted to GenBank.Heloderma_suspectum.final.reference-chrW_PAR-masked.fasta -- Final reference assembly containing the longest autosomes between both haplotypes, the Z and W chromosomes, as well as the mitogenome (i.e. hap1 + chrW + mtDNA). The pseudoautosomal region (PAR) on chrW is hard masked (replaced by "N" characters). Useful for studies conducting interested in read mapping with the intention of calling accurate variants (e.g. indels, SNPs, etc) on the sex chromosomes in female (ZW) samples.Heloderma_suspectum.final.reference.gff3 -- annotation of gene features for the final reference assembly generated by EviAnn (https://github.com/alekseyzimin/EviAnn_release) with RNAseq, Iso-seq, and a custom protein database as evidence. Satellite arrays were hard-masked on chrW prior to gene annotation. Mitogenome annotations were generated via liftoff [v1.6.3] (https://github.com/agshumate/Liftoff) from the reference mitogenome for Heloderma suspectum (NC_008776.1).Heloderma_suspectum.final.reference.assembly-features.bed -- BED file specifying regions of manual genome patching and location of the single remaining gap on chrW.Heloderma_suspectum.final.reference.telo.bed -- BED file specifying locations of terminal telomeres for each chromosome.Heloderma_suspectum.final.reference.PAR.bed -- BED file specifying manually curated locations of the pseudoautosomal regions for both the Z and W chromosomes.Heloderma_suspectum.final.reference.longdust.bed -- BED file specifying Low Complexity Regions (LCRs) in the genome assembly annotated using longdust [v1.4-r97] (https://github.com/lh3/longdust).Heloderma_suspectum.final.reference.aniann.bed -- BED file specifying locations of satellite arrays generated using anianns (https://github.com/marbl/anianns). Also, used to mask chrW prior to gene annotation, i.e. there are currently no gene annotations within these arrays on chrW.Heloderma_suspectum.final.reference.*.longcallD.vcf -- VCF file specifying locations of haplotype-specific small variants and structural variants (SVs) from both ONT and HiFi data using longcallD [v0.0.4] (https://github.com/yangao07/longcallD).Heloderma_suspectum_10-3-25.hap1.HiFi-polished.fasta -- FASTA file containing to complete T2T haplotype assembly for the Gila monster (contains chrZ). Associated manual curation features provided in Heloderma_suspectum_10-3-25.hap1.HiFi-polished.features.bed, repeat elements annotated using EarlGrey in Heloderma_suspectum_10-3-25.hap1.filteredRepeats.gff3, and LCRs in Heloderma_suspectum_10-3-25.hap1.HiFi-polished.longdust.bed (see longdust.bed above).Heloderma_suspectum_10-3-25.hap2.HiFi-polished.fasta -- FASTA file containing to near-complete T2T haplotype assembly for the Gila monster (contains chrW). Associated manual curation features provided in Heloderma_suspectum_10-3-25.hap2.HiFi-polished.features.bed, repeat elements annotated using RepeatMasker using the hap1 EarlGrey library (Heloderma_suspectum_10-3-25.hap1-families.fa.strained.clstrd.fasta.gz) in Heloderma_suspectum_10-3-25.hap2.filteredRepeats.gff3, and LCRs in Heloderma_suspectum_10-3-25.hap2.HiFi-polished.longdust.bed (see longdust.bed above).Initial assembly graph was generated using UL-ONT data only with hifiasm [v0.25.0-r726] (https://github.com/chhylp123/hifiasm) and patched using a separate assembly graph generated using PacBio HiFi and UL-ONT data with verkko [v2.2.1] (https://github.com/marbl/verkko). The assembly was polished using PacBio data aligned to the diploid assembly using minimap2 [v2.28-r1209] (https://github.com/lh3/minimap2) and and freebayes [v1.3.8] (https://github.com/freebayes/freebayes).
Figshare2025-12-04 更新00
Cassiopea xamachana, genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Cassiopea xamachana to facilitate genome assembly and annotation as part of the Aquatic Symbiosis Genomics (ASG) Project (https://www.aquaticsymbiosisgenomics.org/) from samples supplied by the ASG Symbioses-in-3D Hub (https://www.aquaticsymbiosisgenomics.org/collaborators/symbioses-in-3d/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem00
BAW_Whole Genome annotation and assembly
Supplementary data provides further details on this assembly and annotation process. Genome sequencing and assembly of Spodoptera exigua (BAW)
Figshare2023-07-06 更新10
Gambusia holbrooki (eastern mosquitofish), genomic and transcriptomic data. fGamHol
This project collects the genomic and transcriptomic data generated for Gambusia holbrooki to facilitate genome assembly and annotation as part of the Biodiversity Genomics Europe project (BGE, https://biodiversitygenomics.eu/) and organised by the European Reference Genome Atlas (ERGA, https://www.erga-biodiversity.eu/) initiative.
NIAID Data Ecosystem00
Aechmophorus occidentalis (western grebe) genomic and transcriptomic data. Aechmophorus occidentalis
This project collects the genomic and transcriptomic data generated for the western grebe (Aechmophorus occidentalis), to facilitate genome assembly and annotation as part of the Canadian BioGenome Project (https: //www.earthbiogenome.ca/) provided by CGEn - Canada's national platform for genome sequencing and analysis, and its partners. The data under this project are made available subject to the Canadian BioGenome Project Open Data Release Policy.
NIAID Data Ecosystem10
Empis tessellata, genomic and transcriptomic data. idEmpTess
This project collects the genomic and transcriptomic data generated for Empis tessellata to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem10
Mustelus asterias (starry smooth-hound), genomic and transcriptomic data. sMusAst
This project collects the genomic and transcriptomic data generated for Mustelus asterias, common name starry smooth-hound, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem00
Pseudacysta perseae RefSeq Genome. Pseudacysta perseae
Pseudacysta perseae genome reference project
NIAID Data Ecosystem60
Ophion confusus, genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Ophion confusus to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem30
Cirsium dissectum, genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Cirsium dissectum to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem00
Hylaea fasciaria (barred red), genomic and transcriptomic data. ilHylFasc
This project collects the genomic and transcriptomic data generated for Hylaea fasciaria, common name barred red, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem30
Culex laticinctus, genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Culex laticinctus to facilitate genome assembly and annotation as part of the Biodiversity Genomics Europe project (BGE, https://biodiversitygenomics.eu/) and organised by the European Reference Genome Atlas (ERGA, https://www.erga-biodiversity.eu/) initiative.
NIAID Data Ecosystem00
Cakile edentula subsp. lacustris RefSeq Genome. Cakile edentula subsp. lacustris
Cakile edentula subsp. lacustris genome reference project
NIAID Data Ecosystem50
Melanostoma scalare (slender grass hoverfly), genomic and transcriptomic data
This project collects the genomic and transcriptomic data generated for Melanostoma scalare, common name slender grass hoverfly, to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem40
Agriotes lineatus, genomic and transcriptomic data. icAgrLine
This project collects the genomic and transcriptomic data generated for Agriotes lineatus to facilitate genome assembly and annotation as part of the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https://www.darwintreeoflife.org/project-resources/).
NIAID Data Ecosystem00



