cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16459106
title: Kraken2 index of Homo sapiens genome assembly T2T-CHM13v2.0

description: This dataset contains the Kraken2 index for GCF_009914755.1, the Homo sapiens genome assembly T2T-CHM13v2.0.

With the advent of new human reference genomes, the field has progressed beyond the traditional hg19 and hg38 assemblies. The Telomere-to-Telomere (T2T) CHM13v2.0 assembly represents the first complete human genome, providing a gapless and highly accurate reference that spans all chromosomes end-to-end. This new reference overcomes limitations of previous versions by resolving centromeric regions, telomeres, segmental duplications, and other repetitive regions that were previously unresolved or misassembled. As a result, CHM13v2.0 offers improved read alignment, variant calling, and annotation accuracy, especially in previously inaccessible genomic regions—making it an invaluable resource for high-resolution genomic studies.

K-mer–based classification tools, which are significantly faster than traditional read aligners such as BWA, Bowtie2, Minimap2, or BWA-MEM2, often face a major limitation: the difficulty of building a customized index from user-defined FASTA files. These tools rely on additional taxonomy files such as nodes.dmp and names.dmp, which store hierarchical relationships and taxonomic names.

However, for custom references—such as specific human assemblies (e.g., CHM13v2.0) or genomes of unknown or artificial evolutionary origin—such taxonomic information is often unavailable or not applicable, making it impossible to construct a proper index for k-mer–based classification.

To overcome this challenge, we developed a tool named FastaKrakenizer (https://github.com/arpit20328/FastaKrakenizer), a simple Bash script that enables the creation of functional Kraken2-compatible k-mer indices from arbitrary FASTA files without requiring external taxonomy files. This broadens the applicability of k-mer–based classification to a wider range of genomic references.

The tool allows rapid identification and quantification of sequencing reads mapped to a custom FASTA reference, facilitating downstream analysis for researchers in the fields of genomics and computational biology.

As an example, the Kraken2 index for the T2T-CHM13v2.0 human genome assembly (GCF_009914755.1) is provided here as a compressed .tar.gz archive.

For questions, suggestions, or issues, please visit our GitHub repository and open an issue in the Issues section: https://github.com/arpit20328/FastaKrakenizer
DOI: 10.5281/zenodo.16459107
title: Kraken2 index of Homo sapiens genome assembly T2T-CHM13v2.0

description: This dataset contains the Kraken2 index for GCF_009914755.1, the Homo sapiens genome assembly T2T-CHM13v2.0.

With the advent of new human reference genomes, the field has progressed beyond the traditional hg19 and hg38 assemblies. The Telomere-to-Telomere (T2T) CHM13v2.0 assembly represents the first complete human genome, providing a gapless and highly accurate reference that spans all chromosomes end-to-end. This new reference overcomes limitations of previous versions by resolving centromeric regions, telomeres, segmental duplications, and other repetitive regions that were previously unresolved or misassembled. As a result, CHM13v2.0 offers improved read alignment, variant calling, and annotation accuracy, especially in previously inaccessible genomic regions—making it an invaluable resource for high-resolution genomic studies.

K-mer–based classification tools, which are significantly faster than traditional read aligners such as BWA, Bowtie2, Minimap2, or BWA-MEM2, often face a major limitation: the difficulty of building a customized index from user-defined FASTA files. These tools rely on additional taxonomy files such as nodes.dmp and names.dmp, which store hierarchical relationships and taxonomic names.

However, for custom references—such as specific human assemblies (e.g., CHM13v2.0) or genomes of unknown or artificial evolutionary origin—such taxonomic information is often unavailable or not applicable, making it impossible to construct a proper index for k-mer–based classification.

To overcome this challenge, we developed a tool named FastaKrakenizer (https://github.com/arpit20328/FastaKrakenizer), a simple Bash script that enables the creation of functional Kraken2-compatible k-mer indices from arbitrary FASTA files without requiring external taxonomy files. This broadens the applicability of k-mer–based classification to a wider range of genomic references.

The tool allows rapid identification and quantification of sequencing reads mapped to a custom FASTA reference, facilitating downstream analysis for researchers in the fields of genomics and computational biology.

As an example, the Kraken2 index for the T2T-CHM13v2.0 human genome assembly (GCF_009914755.1) is provided here as a compressed .tar.gz archive.

For questions, suggestions, or issues, please visit our GitHub repository and open an issue in the Issues section: https://github.com/arpit20328/FastaKrakenizer
DOI: 10.15468/dl.mqwvws
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aleurodicus rugioperculatus",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052021-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpgaek
title: Occurrence Download

description: A dataset containing 533308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Vicia sativa"
 ]
}

 The dataset includes 533308 records from 3108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051929-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cqx3jx
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Petroleuciscus borysthenicus",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 40 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011804-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekuy2z
title: Occurrence Download

description: A dataset containing 11251 species occurrences available in GBIF matching the query:
{
 "PublishingOrg" : [
 "is 28d17f8f-39f3-4041-9734-67c4f1e7693e"
 ]
}

 The dataset includes 11251 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011803-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekvuyp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ateles paniscus (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214504-220831081235567/datasets/export for details.
DOI: 10.15468/dl.6qdfvn
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Ethiopia, Tanzania, United Republic of, Kenya, Rwanda, South Africa, Madagascar, Cameroon, Congo, Democratic Republic of the, Malawi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EX, EW, EN, CR, VU, NT, LC, DD, NE)",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, a344ee9f-f1b7-4761-be2c-58ee6d741395, 061b4f20-f241-11da-a328-b8a03c50a862, bc092ff0-02e4-11dc-991f-b8a03c50a862, 396d5f30-dea9-11db-8ab4-b8a03c50a862, c76cf030-2a95-11da-9cc1-b8a03c50a862, 45a451cf-a94a-4df0-9511-1dca805a97db, 2cd829bb-b713-433d-99cf-64bef11e5b3e, 19456090-b49a-11d8-abeb-b8a03c50a862, da86174a-a605-43a4-a5e8-53d484152cd3)",
 "TaxonKey is Helichrysum chionoides Philipson"
 ]
}

 The dataset's 1 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0265690-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2kzk4
title: Occurrence Download

description: A dataset containing 863 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Artemisia argyi H.Lév. & Vaniot"
 ]
}

 The dataset includes 863 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001323-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3yuy4p
title: Occurrence Download

description: A dataset containing 842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.95662 41.27526,0.94558 41.26302,0.94491 41.24417,0.95279 41.23786,0.98808 41.23929,1.00138 41.25536,1.00513 41.27241,0.99146 41.27894,0.96533 41.27999,0.95662 41.27526))",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 842 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214497-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zwpfa6
title: Occurrence Download

description: A dataset containing 9889 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panulirus interruptus (J.W.Randall, 1840)"
 ]
}

 The dataset includes 9889 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242801-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zd5euh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spirostreptida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257511-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.63q5nd
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scarus obishime Randall & Earle, 1993"
 ]
}

 The dataset includes 66 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242803-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6mv47
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-96.71126 15.70939,-96.67734 15.70939,-96.67734 15.73287,-96.71126 15.73287,-96.71126 15.70939))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 290 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214514-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gp7q46
title: Occurrence Download

description: A dataset containing 5223332 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-88.5898 14.74718,-79.65876 14.74718,-79.65876 22.042,-88.5898 22.042,-88.5898 14.74718))"
 ]
}

 The dataset includes 5223332 records from 1067 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0242798-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.prq3an
title: Occurrence Download

description: A dataset containing 4252 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oenothera perennis L."
 ]
}

 The dataset includes 4252 records from 170 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001305-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.av23ub
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Miniopterus fuscus Bonhote, 1902",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214499-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pysjvd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Antilocapra americana (Ord, 1815)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214506-220831081235567/datasets/export for details.
DOI: 10.15468/dl.w9hv8x
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rohdea fimbriata (Hand.-Mazz.) Yamashita & M.N.Tamura"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0243400-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5j745n
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prunus mongolica Maxim."
 ]
}

 The dataset includes 55 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0250476-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcx5f5
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dipterocarpus alatus Roxb.",
 "Year 2000-2024"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066550-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9vr7pc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sicista caudata Thomas, 1907",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214508-220831081235567/datasets/export for details.
DOI: 10.15468/dl.5fxvna
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Felis silvestris Schreber, 1777",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214515-220831081235567/datasets/export for details.
DOI: 10.15468/dl.rf9mxm
title: Occurrence Download

description: A dataset containing 1389 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Brassica rapa var. oleifera DC."
 ]
}

 The dataset includes 1389 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0243403-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hhujuu
title: Occurrence Download

description: A dataset containing 4134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Buthidae)",
 "HasCoordinate is true",
 "Geometry POLYGON((-81 -35, -34 -35, -34 13, -81 13, -81 -35))"
 ]
}

 The dataset includes 4134 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001327-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.997yv2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corythaeola cristata (Vieillot, 1816)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214507-220831081235567/datasets/export for details.
DOI: 10.15468/dl.9fdvxh
title: Occurrence Download

description: A dataset containing 583256 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Vulpes vulpes (Linnaeus, 1758)"
 ]
}

 The dataset includes 583256 records from 2051 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0250461-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fqmucv
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AED3866"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002084-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vj32bd
title: Occurrence Download

description: A dataset containing 4792781 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Rodentia, Chiroptera)"
 ]
}

 The dataset includes 4792781 records from 543 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002071-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzz5md
title: Occurrence Download

description: A dataset containing 930 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trichopodus trichopterus)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 930 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002085-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cyzqfp
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AED3865"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002086-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wsn7p9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of ()",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002088-250711103210423/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12445671
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.86a73c
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apteronotus rostratus"
 ]
}

 The dataset includes 121 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002089-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n3r6vd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of ()",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002090-250711103210423/datasets/export for details.
DOI: 10.15468/dl.phec4m
title: Occurrence Download

description: A dataset containing 101117 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Xema sabini)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 101117 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002076-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7k2bv8
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AAF5553"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002091-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15858115
title: STUDY AND WORK IN THE LIVES OF COMPUTING STUDENTS

description: [en]

STUDY AND WORK IN THE LIVES OF COMPUTING STUDENTS

This data was extracted from an educational study that systematically examines the challenges experienced by computing students who are employed while pursuing their studies.

[pt]

ESTUDO E TRABALHO NA VIDA DE ESTUDANTES DE COMPUTAÇÃO

Dados extraídos de um estudo educacional sobre os desafios enfrentados por estudantes de computação que conciliam trabalho e estudo.