cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0026947.10fu
title: SH0026947.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0026948.10fu
title: SH0026948.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/rzl-7hz-xae
title: Myriophyllum sibiricum Kom.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.18022756
title: Genotyping Pipeline Reference Data v1.0

description: Genotyping Pipeline - Reference Data


 



Overview


This Zenodo repository contains pre-built reference files for the Genotyping Pipeline, a Nextflow-based workflow for genotype imputation, quality control, and ancestry inference.



Files Included




1. TOPMed PASS Variants Reference (3.8 GB)


File: PASS.Variants.TOPMed_freeze10_hg38.tab.gz

Pre-formatted variant summary from BRAVO TOPMed Freeze 10, containing only PASS-filtered variants (756M variants) in Rayner/McCarthy format for use with the HRC-1000G-check-bim.pl strand-checking script.

Format (8 columns):



CHR  POS  ID  REF  ALT  AC  AN  AF
1    10019  rs775809821  TA  T  6  301798  1.98823e-05
1    10039  rs978760828  A   C  8  301798  2.65097e-05
...


 


Usage: Pre-imputation QC to check strand alignment and identify problematic variants.

 

 



 




Option 2: Manual Download




# Download directly from Zenodo
wget https://zenodo.org/records/XXXXXXX/files/PASS.Variants.TOPMed_freeze10_hg38.tab.gz

# Place in resources directory
mv PASS.Variants.TOPMed_freeze10_hg38.tab.gz resources/rayner/

 






Data Sources





File
Source
License




TOPMed PASS Variants
BRAVO
Public summary statistics


1KG Reference
1000 Genomes
Fort Lauderdale Agreement


HGDP Reference
HGDP
Public






Citation


If you use this data, please cite:





This pipeline:



Magyar C, et al. (2025). Genotyping Pipeline: A Nextflow workflow for genotype imputation and ancestry inference. Zenodo. https://doi.org/10.5281/zenodo.18022757

TOPMed:







Taliun D, et al. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature, 590(7845), 290-299.





1000 Genomes:



The 1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature, 526(7571), 68-74.






Related Resources




GitHub Repository: https://github.com/chrisrob3312/genotyping_pipeline

Documentation: https://github.com/chrisrob3312/genotyping_pipeline/wiki

Containers (Sylabs): library://chrisrob3312/genotyping_pipeline




Version History





Version
Date
Changes




1.0.0
2025-12-22
Initial release with TOPMed PASS variants






Contact


For questions or issues:



Open an issue on GitHub

Email: [christina.magyar@bcm.edu]




License


The reference data files are provided under their original licenses (see Data Sources above).
DOI: 10.5281/zenodo.18022757
title: Genotyping Pipeline Reference Data v1.0

description: Genotyping Pipeline - Reference Data


 



Overview


This Zenodo repository contains pre-built reference files for the Genotyping Pipeline, a Nextflow-based workflow for genotype imputation, quality control, and ancestry inference.



Files Included




1. TOPMed PASS Variants Reference (3.8 GB)


File: PASS.Variants.TOPMed_freeze10_hg38.tab.gz

Pre-formatted variant summary from BRAVO TOPMed Freeze 10, containing only PASS-filtered variants (756M variants) in Rayner/McCarthy format for use with the HRC-1000G-check-bim.pl strand-checking script.

Format (8 columns):



CHR  POS  ID  REF  ALT  AC  AN  AF
1    10019  rs775809821  TA  T  6  301798  1.98823e-05
1    10039  rs978760828  A   C  8  301798  2.65097e-05
...


 


Usage: Pre-imputation QC to check strand alignment and identify problematic variants.

 

 



 




Option 2: Manual Download




# Download directly from Zenodo
wget https://zenodo.org/records/XXXXXXX/files/PASS.Variants.TOPMed_freeze10_hg38.tab.gz

# Place in resources directory
mv PASS.Variants.TOPMed_freeze10_hg38.tab.gz resources/rayner/

 






Data Sources





File
Source
License




TOPMed PASS Variants
BRAVO
Public summary statistics


1KG Reference
1000 Genomes
Fort Lauderdale Agreement


HGDP Reference
HGDP
Public






Citation


If you use this data, please cite:





This pipeline:



Magyar C, et al. (2025). Genotyping Pipeline: A Nextflow workflow for genotype imputation and ancestry inference. Zenodo. https://doi.org/10.5281/zenodo.18022757

TOPMed:







Taliun D, et al. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature, 590(7845), 290-299.





1000 Genomes:



The 1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature, 526(7571), 68-74.






Related Resources




GitHub Repository: https://github.com/chrisrob3312/genotyping_pipeline

Documentation: https://github.com/chrisrob3312/genotyping_pipeline/wiki

Containers (Sylabs): library://chrisrob3312/genotyping_pipeline




Version History





Version
Date
Changes




1.0.0
2025-12-22
Initial release with TOPMed PASS variants






Contact


For questions or issues:



Open an issue on GitHub

Email: [christina.magyar@bcm.edu]




License


The reference data files are provided under their original licenses (see Data Sources above).
DOI: 10.15156/bio/sh0026949.10fu
title: SH0026949.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/9cj-gas-56a
title: Myriophyllum sibiricum Kom.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/mek-480-7jb
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/3qx-g4b-kp4
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/pc1-f2g-alc
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026950.10fu
title: SH0026950.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/qmm-maq-z9j
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s2g-lh1-k8p
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026951.10fu
title: SH0026951.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/5df-5ts-5ec
title: Viola canina subsp. ruppii (All.) Schübl. & G. Martens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026952.10fu
title: SH0026952.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/5yf-z2p-jm1
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ter-nfs-mm7
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026953.10fu
title: SH0026953.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/c1x-edk-6l0
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/x1q-yna-73l
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/41g-27v-4q0
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/5rg-fyp-00p
title: Viola canina subsp. ruppii (All.) Schübl. & G. Martens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026954.10fu
title: SH0026954.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.3535/3xc-y2w-7ny
title: Viola canina subsp. ruppii (All.) Schübl. & G. Martens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/41d-3lw-5lg
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/94e-54c-d1z
title: Cornus suecica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/cnt-lsw-ers
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15156/bio/sh0026955.10fu
title: SH0026955.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.x3eaen
title: Occurrence Download

description: A dataset containing 2821 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhinolophus pusillus, Rhinolophus robinsoni, Rhinolophus shameli, Rhinolophus siamensis, Rhinolophus sinicus, Rhinolophus stheno, Rhinolophus thomasi, Arielulus circumdatus, Barbastella darjelingensis, Eptesicus pachyomus, Eudiscopus denticulus, Glischropus bucephalus, Harpiocephalus harpia, Harpiola isodon, Hesperoptenus blanfordi, Hesperoptenus tickelli, Hypsugo cadornae, Hypsugo dolichodon, Hypsugo joffrei, Hypsugo pulveratus, Ia io, Kerivoula depressa, Kerivoula dongduongana, Kerivoula furva, Kerivoula hardwickii, Kerivoula kachinensis, Kerivoula papillosa, Kerivoula picta, Kerivoula titania, Murina annamitica, Murina beelzebub, Murina chrysochaetes, Murina cyclotis, Murina eleryi, Murina feae, Murina fionae, Murina harpioloides, Murina harrisoni, Murina huttonii, Murina leucogaster, Murina walstoni, Myotis altarium, Myotis annamiticus, Myotis annatessae, Myotis annectans, Myotis ater, Myotis chinensis, Myotis formosus, Myotis hasseltii, Myotis horsfieldii)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 2821 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075129-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/2ze-ehn-mlh
title: Viola palustris L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/enc-gwg-f90
title: Viola canina subsp. ruppii (All.) Schübl. & G. Martens

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.15468/dl.gyce4v
title: Occurrence Download

description: A dataset listing the 36 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-106.55002 34.92249,-106.12748 34.86581,-106.12748 35.40558,-106.58352 35.42104,-106.52297 35.12088,-106.55002 34.92249))",
 "TaxonKey is Fungi",
 "Year 2015-2020"
 ]
}

 The dataset's 36 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008574-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mv6b9q
title: Occurrence Download

description: A dataset containing 12493 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nonea pulla (L.) DC."
 ]
}

 The dataset includes 12493 records from 238 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008576-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6j6h48
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Flora of the Korean Peninsula Phase II",
 "TaxonKey is Fallopia multiflora var. ciliinervis (Nakai) Yonek. & H.Ohashi"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008577-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w2gz4q
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is one of (Portugal, Spain)",
 "Geometry POLYGON((-8.83397 41.06975,-8.37709 41.04242,-8.46592 43.12652,-9.14102 42.79105,-8.83397 41.06975))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fagus L.",
 "Year 2004-2024"
 ]
}

 The dataset's 1 records were derived from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008575-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tt2pfg
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-106.55002 34.92249,-106.12748 34.86581,-106.13195 35.2382,-106.12748 35.40558,-106.58352 35.42104,-106.52297 35.12088,-106.55002 34.92249))",
 "TaxonKey is Fungi",
 "Year 2021-2024"
 ]
}

 The dataset includes 299 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008579-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14251139
title: kassina_somalica_zanfona_1.fasta.gz
DOI: 10.5281/zenodo.14251140
title: kassina_somalica_zanfona_1.fasta.gz
DOI: 10.15468/dl.x492xm
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is one of (Portugal, Spain)",
 "Geometry POLYGON((-8.83397 41.06975,-8.37709 41.04242,-8.46592 43.12652,-9.14102 42.79105,-8.83397 41.06975))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Fraxinus Tourn. ex L.",
 "Year 2004-2024"
 ]
}

 The dataset includes 242 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008581-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14251145
title: kinnapotiguara_troglobia_zanfona_1.fasta.gz
DOI: 10.5281/zenodo.14251146
title: kinnapotiguara_troglobia_zanfona_1.fasta.gz