Batch Download

Users can download the genome files used to construct the pangenome here.

AQLBahu1hap.fa.gz AQLBahu2hap.fa.gz AQLBont.fa.gz AQLBzj1hap.fa.gz AQLBzj2hap2.fa.gz AW1hap.fa.gz AW2hap.fa.gz Babraham.fa.gz Bama1hap.fa.gz Bama2hap.fa.gz Bamei.fa.gz Banna1hap.fa.gz Banna2hap.fa.gz Berk1Tibet.fa.gz Berk2Tibet.fa.gz Berk3Tibet.fa.gz Berk4Tibet.fa.gz BerkGXv1.fa.gz BerkGXv2.fa.gz Berkshire1hap.fa.gz Berkshire2hap.fa.gz Chenghua1hap.fa.gz Chenghua2hap.fa.gz CLH1hap.fa.gz CLH2hap.fa.gz DH1hap.fa.gz DH2hap.fa.gz Diannanxiaoear.fa.gz duroc.fa.gz DurocLiGv1.fa.gz DurocLiGv2.fa.gz EB51hap.fa.gz EB52hap.fa.gz EHL1hap.fa.gz EHL2hap.fa.gz EW.fa.gz GZB1hap.fa.gz GZB2hap.fa.gz HJB1hap.fa.gz HJB2hap.fa.gz Huai.fa.gz JH1hap.fa.gz JH2hap.fa.gz JianLi1hap.fa.gz JianLi2hap.fa.gz Jinhuaont.fa.gz JinhuaT2T.fa.gz Juema1hap.fa.gz Juema2hap.fa.gz JXH1hap.fa.gz JXH2hap.fa.gz Laiwuclr.fa.gz Laiwuont.fa.gz LaiWzj1hap.fa.gz LaiWzj2hap.fa.gz Landrace1hap.fa.gz Landrace2hap.fa.gz LandraceT2T.fa.gz Lantang1hap.fa.gz Lantang2hap.fa.gz Largewhiteyu1hap.fa.gz Largewhiteyu2hap.fa.gz Luchuan.fa.gz LWTang1hap.fa.gz LWTang2hap.fa.gz Meishanliu.fa.gz Meishanont.fa.gz MeishanV1.fa.gz Minont.fa.gz MinT2T.fa.gz MSjxau.fa.gz MZ1hap.fa.gz MZ2hap.fa.gz Nanchukmacdon.fa.gz Neijiang.fa.gz NingXiang.fa.gz PI1hap.fa.gz PI2hap.fa.gz Piet1hap.fa.gz Piet2hap.fa.gz Rongchangont.fa.gz RongchangT2T.fa.gz SB1hap.fa.gz SB2hap.fa.gz SS1hap.fa.gz SS2hap.fa.gz SWT1hap.fa.gz SWT2hap.fa.gz Tabasco.fa.gz Tibetan1hap.fa.gz Tibetan2hap.fa.gz Tibetanont.fa.gz Tongcheng.fa.gz Tunchang1hap.fa.gz Tunchang2hap.fa.gz WildboarVeluwe.fa.gz Wisconsin.fa.gz Wuzhishanont.fa.gz WuzhishanT2T.fa.gz WZSzj1hap.fa.gz WZSzj2hap.fa.gz XJHZ1hap.fa.gz XJHZ2hap.fa.gz Y1hap.fa.gz Y2hap.fa.gz YorkErHv1.fa.gz YorkErHv2.fa.gz Yorkshireont.fa.gz

Users can download the original graphical pan-genome files based on T2T-Sscrofa, T2T-Bamei, and Sscrofa11.1 as reference genomes here.

T2T-Sscrofa.pangenome.primates-pg.gfa.gz T2T-Bamei.pangenome.primates-pg.gfa.gz T2T-Sscrofa.pangenome.primates-pg.gfa.gz

Users can access genome assemblies and annotations of T2T Duroc, T2T Bamei, Asian wild boar, and Veluwe wild boar. Both sequence (.fa.gz) and gene annotation (.gtf.gz) files are available for download.

Genome version	Asianwildboar genome	Asianwildboar annotation	T2T_Bamei genome	T2T_Bamei annotation	T2T_Sscrofa genome	T2T_Sscrofa annotation	WildboarVeluwe genome	WildboarVeluwe annotation
T2T_Sscrofa_Genomes	Asianwildboar.genomic.fa.gz (626M)	Asianwildboar.genomic.gtf.gz (29M)	T2T_Bamei.fa.gz (670M)	T2T_Bamei.genomic.gtf.gz (23M)	T2T_Sscrofa.fa.gz (673M)	T2T_Sscrofa.genomic.gtf.gz (26M)	WildboarVeluwe.fa.gz (677M)	WildboarVeluwe.genomic.gtf.gz (26M)

Dong Li, Yulong Wang, Tiantian Yuan, Minghao Cao, et al 2024. Pangenome and genome variations analyses of pigs unveil genomic facets for their adaptation and agronomic characteristics. iMeta 3: e257.

Users can download data sets of pig pangenome gfa file, pangenome vcf file, Pangenie structural variation vcf file, and pangenome sequence file from Minigraph-Cactus. The genome annotation of Bamei, Juema, Hanjiang Black, and Large White are also provided. Please choose your desired files to download in following.

Genome version	pangenome sequence file from Minigraph-Cactus	pangenome gfa file	Pangenie structural variation vcf file	Bamei genome annotation	Juema genome annotation	Hanjiang Black genome annotation	Large White genome annotation	Pan-sequences location
Graph_panPig	Minigraph_Cactus_Pangenie_Sur.vcf.gz (98M)	pig18chr.full.gfa.gz (6.9G)	pig18chr.vcf.gz (2.1G)	Bamei.gtf.gz (42M)	Hanjiangblack.gtf.gz (34M)	Juema.gtf.gz (43M)	LargeWhite.gtf.gz (35M)	pan-sequences.27genome.fa.gz (82M)

Tian X, Li R, Fu W, et al. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data[J]. Science China. Life sciences, 2020, 63(5):750-763.

Users can download data sets of panPig_v1 assembly, pan-sequences annotation, copy number variation regions (CNVR), gene expression and chromosome localization of pan-sequences. Please choose your desired files to download in following table.

Genome version	Pan-genome reference	Pan-sequences set	Male-specific sequences set	Pan-sequences annotation	Copy number variations	Gene expression	Pan-sequences location
panPig_v1	panPig_v1.dna.tar.gz (783M)	pan-sequences.fa.gz (21M)	Male-specific.fq.gz (3.0M)	pan-sequences.gff.tar.gz (948K)	panPig.CNVR.gz (6.0M)	panPig.trans.gz (4.4M)	pan-sequences.location.gz (596K)