NextGen

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

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

De novo assemblies

• Assembled using Allpaths-LG
• Genomic alignments to the domestic species used Ensembl pairwise alignment analysis

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.

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".