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NextGen is a collaborative research project investigating the biodiversity of livestock species. NextGen used whole genome sequencing and genotyping microarrays to catalogue and study variation within populations of cattle, sheep and goat.

NextGen project genomic data sets are publicly available:

  • Cattle, sheep and goats sampled
  • Whole genome sequencing for hundreds of samples
  • Genotyping microarrays for hundreds more samples
  • Domesticated and wild-type ancestral species
  • Traditional breeds and industrial breeds
  • Samples from Iran, Morocco and Uganda
  • De novo genome assemblies of wild species

WGS Variation Data

Population Species Country Samples Variant Discovery Variants Genus level SNPs
IRBT Bos taurus (cattle) Iran9 vcf | browse | vep 20.1 M vcf | browse | vep
UGBT Bos taurus × indicus (cattle) Uganda25 vcf | browse | vep 29.3 M vcf | browse | vep
IROA Ovis aries (sheep) Iran20 vcf | browse | vep 25.8 M vcf | browse | vep
IROO Ovis orientalis (mouflon) Iran19 vcf | browse | vep 29.3 M vcf | browse | vep
MODA Ovis aries (sheep) Morocco160 vcf | browse | vep 38.5 M vcf | browse | vep
ISGC Ovis aries (sheep) (various)175 vcf | browse | vep
IROV Ovis vignei (urial) Iran4 vcf | browse | vep
IRCA Capra aegagrus (bezoar) Iran22 vcf | vep 17.4 M vcf | vep
IRCH Capra hircus (goat) Iran20 vcf | vep 22.9 M vcf | vep
MOCH Capra hircus (goat) Morocco161 vcf | vep 31.8 M vcf | vep
AUCH Capra hircus (goat) Australia25 vcf | vep
AUFR Capra hircus (goat) France4 vcf | vep
ITCH Capra hircus (goat) Italy35 vcf | vep
Variant Discovery
All SNPs and indels discovered from whole genome sequencing that passed the NextGen quality filters.
Genus level SNPs
Genotypes re-called at all known SNP sites within the genus. Intended for cross-species and cross-population comparisons.
VEP
Variant call sets were annotated with the Variant Effect Predictor.

1. [Seventy-five sheep from many different countries were were sequenced by the International Sheep Genomics Consortium (ISGC) and analysed by NextGen]
2. [Five Australian Capra hircus were sequenced by CSIRO and analysed by NextGen]
3. [Five Italian Capra hircus were sequenced by the project Genhome and were contributed to the Nextgen project by PTP and IBBA-CNR]

Microarray Data

Species Country Array Samples Genotypes
Bos taurus × indicus (cattle) UgandabovineHD102 vcf | browse
Bos taurus × indicus (cattle) UgandabovineSNP50813 vcf | browse
Ovis orientalis (mouflon) IranovineSNP508 vcf | browse
Ovis aries (sheep) IranovineSNP5018 vcf | browse
Ovis aries (sheep) MoroccoovineSNP5030 vcf | browse
Capra aegagrus (bezoar) IrangoatSNP507 vcf
Capra hircus (goat) IrangoatSNP509 vcf
Capra hircus (goat) MoroccogoatSNP5030 vcf

De novo assemblies

Ovis orientalis Capra aegagrus
Species mouflon (wild sheep) bezoar (wild goat)
Assembly nameOori1Caeg1
ENA project PRJEB3141 PRJEB3140
Assembled scaffolds fasta | repeat mask fasta fasta | repeat mask fasta
Number of Scaffolds6,1736,616
Total scaffold length2.59 Gbp2.58 Gbp
Scaffold N502.21 Mbp1.75 Mbp
Genomic alignment to domestic species vs sheep OARv3.1 vs goat CHIR1.0
More assembly information Readme Readme
More genomic alignment information Readme Readme

Available Data

The European Nucleotide Archive contains:

  • Fastq: Whole genome Illumina sequencing.
  • Bam: Reads aligned to the reference assemblies, with indel realignment and marked duplicates.
  • Assemblies: De novo genomes of mouflon and bezoar.

The European Variation Archive contains:

  • Variant call sets: From WGS and microarray data
  • File formats: vcf and ped/map formats, with VEP annotation

The NextGen ftp site contains multifarious data, including:

  • Sample indexes: Including animals' location, breed, age.
  • Documentation: E.g. how to find data, and NextGen's data processing methods.
  • Photographs: Images of sampled animals.
  • Links to archived data: Fastq, bam, genome assemblies, variant calls
  • Preprocessed data: E.g. unfiltered WGS variant calls, raw microarray data.

Data Reuse

Please observe NextGen's policy on data reuse.

EU Logo The research leading to these results received funding from the European Union's Seventh Framework Programme (FP7/2010-2014) under grant agreement no 244356 - "NextGen".