Batch Download

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)

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)

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)

 

Genus	Species/Breed	Genome name	Assembly level	Contig N50	Scaffold N50	Total sequence length	Download link
Sus scrofa (pig)	Anqingliuwhite	Anqingliuwhite_ont	Chromosome	64,914,856	140,847,541	2,468,275,601	Anqingliuwhite.fa.gz
Sus scrofa (pig)	Asianwild	Asianwild_hifi	Chromosome	121,312,963	140,690,000	2,709,177,899	Asianwild.fa.gz
Sus scrofa (pig)	Asianwild	Asianwild_hifi_hap1	Chromosome	112,032,033	148,227,338	2,664,155,311	Asianwild.hap1.fa.gz
Sus scrofa (pig)	Asianwild	Asianwild_hifi_hap2	Chromosome	107,167,819	147,836,305	2,658,017,286	Asianwild.hap2.fa.gz
Sus scrofa (pig)	Babraham	Babraham_clr	Chromosome	34,950,000	139,230,000	2,447,663,892	Babraham.fa.gz
Sus scrofa (pig)	Bama	Bama_hifi	Chromosome	109,197,835	146,516,085	2,705,731,770	Bamahifi.fa.gz
Sus scrofa (pig)	Bama	Bama_hifi_hap1	Chromosome	72,603,881	142,482,536	2,560,446,855	Bamahifi.hap1.fa.gz
Sus scrofa (pig)	Bama	Bama_hifi_hap2	Chromosome	86,431,712	144,894,958	2,584,884,868	Bamahifi.hap2.fa.gz
Sus scrofa (pig)	Banna	Banna_hifi	Chromosome	87,772,251	140,878,000	2,659,554,321	Banna.fa.gz
Sus scrofa (pig)	Banna	Banna_hifi_hap1	Chromosome	84,664,492	141,453,458	2,593,204,768	Banna.hap1.fa.gz
Sus scrofa (pig)	Banna	Banna_hifi_hap2	Chromosome	84,738,186	137,404,524	2,626,382,807	Banna.hap2.fa.gz
Sus scrofa (pig)	Berkshire	Berkshire_hifi	Chromosome	88,996,272	141,237,921	2,679,458,008	Berkshire.fa.gz
Sus scrofa (pig)	Berkshire	Berkshire_hifi_hap1	Chromosome	87,165,761	141,208,000	2,492,162,080	Berkshire1hap.fa.gz
Sus scrofa (pig)	Berkshire	Berkshire_hifi_hap2	Chromosome	85,136,472	139,642,879	2,586,734,099	Berkshire2hap.fa.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet1_ont	Chromosome	55,282,673	139,805,811	2,460,083,238	Berk_Tibet1.fa.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet2_ont	Chromosome	49,968,585	138,449,114	2,426,786,076	Berk_Tibet2.fa.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet3_ont	Chromosome	62,539,042	139,570,799	2,446,192,989	Berk_Tibet3.fa.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet4_ont	Chromosome	55,428,225	139,395,791	2,449,215,793	Berk_Tibet4.fa.gz
Sus scrofa (pig)	Europeanwild	Europeanwild_ont	Chromosome	59,845,970	143,111,967	2,444,796,783	CentralEuropeanwild.fa.gz
Sus scrofa (pig)	Chenghua	Chenghua_hifi	Chromosome	83,223,543	144,489,072	2,714,788,446	Chenghua.fa.gz
Sus scrofa (pig)	Chenghua	Chenghua_hifi_hap1	Chromosome	98,670,375	146,598,848	2,589,877,749	Chenghua.hap1.fa.gz
Sus scrofa (pig)	Chenghua	Chenghua_hifi_hap2	Chromosome	91,362,134	149,244,507	2,566,392,233	Chenghua.hap2.fa.gz
Sus scrofa (pig)	Diannanxiaoear	Diannanxiaoear_clr	Chromosome	14,070,000	137,350,000	2,648,650,142	Diannanxiaoear.fa.gz
Sus scrofa (pig)	Guanzhongblack	Guanzhongblack_hifi	Chromosome	90,934,270	142,867,889	2,659,336,773	Guanzhongblack.fa.gz
Sus scrofa (pig)	Guanzhongblack	Guanzhongblack_hifi_hap1	Chromosome	67,479,456	144,852,998	2,589,296,822	Guanzhongblack.hap1.fa.gz
Sus scrofa (pig)	Guanzhongblack	Guanzhongblack_hifi_hap2	Chromosome	64,330,711	141,897,710	2,629,043,269	Guanzhongblack.hap2.fa.gz
Sus scrofa (pig)	Hanjiangblack	Hanjiangblack_hifi	Chromosome	103,798,690	143,921,899	2,728,369,414	Hanjiangblack.fa.gz
Sus scrofa (pig)	Hanjiangblack	Hanjiangblack_hifi_hap1	Chromosome	69,069,494	143,256,321	2,607,283,817	Hanjiangblack.hap1.fa.gz
Sus scrofa (pig)	Hanjiangblack	Hanjiangblack_hifi_hap2	Chromosome	68,189,243	143,752,490	2,613,988,401	Hanjiangblack.hap2.fa.gz
Sus scrofa (pig)	Huai	Huai_clr	Chromosome	48,211,639	139,366,899	2,455,355,646	Huai.fa.gz
Sus scrofa (pig)	Jinhua	Jinhua_ont	Chromosome	55,190,857	141,068,143	2,457,854,962	Jinhua_ont.fa.gz
Sus scrofa (pig)	Jinhua	jinhua_T2T	Chromosome	100,500,000	142,700,000	2,612,303,023	JinhuaT2T.fa.gz
Sus scrofa (pig)	Juema	Juema_hifi	Chromosome	107,533,513	140,906,000	2,747,610,554	Juema.fa.gz
Sus scrofa (pig)	Juema	Juema_hifi_hap1	Chromosome	90,529,812	145,535,019	2,669,245,476	Juema.hap1.fa.gz
Sus scrofa (pig)	Juema	Juema_hifi_hap2	Chromosome	107,084,359	146,477,985	2,524,228,709	Juema.hap2.fa.gz
Sus scrofa (pig)	Laiwu	Laiwu_clr	Chromosome	37,926,907	140,382,494	2,452,680,395	Laiwu_clr.fa.gz
Sus scrofa (pig)	Laiwu	Laiwu_ont	Chromosome	53,308,730	140,086,223	2,459,422,509	Laiwu_ont.fa.gz
Sus scrofa (pig)	Landrace	Landrace_hifi	Chromosome	91,861,099	143,903,093	2,682,201,977	Landrace_hifi.fa.gz
Sus scrofa (pig)	Landrace	Landrace_hifi_hap1	Chromosome	82,191,483	144,602,316	2,551,349,487	Landrace_hifi.hap1.fa.gz
Sus scrofa (pig)	Landrace	Landrace_hifi_hap2	Chromosome	74,752,263	143,985,561	2,565,484,361	Landrace_hifi.hap2.fa.gz
Sus scrofa (pig)	Landrace	Landrace_T2T	Chromosome	142,100,000	142,100,000	2,633,805,232	LandraceT2T.fa.gz
Sus scrofa (pig)	Lantang	Lantang_hifi	Chromosome	111,351,275	150,483,906	2,679,759,824	Lantang.fa.gz
Sus scrofa (pig)	Lantang	Lantang_hifi_hap1	Chromosome	101,280,242	143,887,179	2,612,727,139	Lantang.hap1.fa.gz
Sus scrofa (pig)	Lantang	Lantang_hifi_hap2	Chromosome	102,474,239	144,865,775	2,629,249,142	Lantang.hap2.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev1_hifi	Chromosome	115,027,642	143,417,155	2,686,811,046	Largewhite_hifi.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev1_hifi_hap1	Chromosome	128,407,102	147,074,298	2,650,613,311	Largewhite_hifi.hap1.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev1_hifi_hap2	Chromosome	112,602,777	143,601,051	2,609,127,809	Largewhite_hifi.hap2.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev2_hifi	Chromosome	81,334,576	143,716,155	2,686,788,046	Largewhite_hifi_V2.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev2_hifi_hap1	Chromosome	44,248,107	140,163,017	2,526,053,051	Largewhite_hifi_V2.hap1.fa.gz
Sus scrofa (pig)	Largewhite	Largewhitev2_hifi_hap2	Chromosome	45,715,522	139,513,711	2,509,768,023	Largewhite_hifi_V2.hap2.fa.gz
Sus scrofa (pig)	Luchuan	Luchuan_clr	Chromosome	37,423,561	138,876,115	2,435,118,017	Luchuan.fa.gz
Sus scrofa (pig)	Meishan	Meishan_clr	Chromosome	46,272,787	139,496,851	2,454,898,984	Meishan_clr.fa.gz
Sus scrofa (pig)	Meishan	Meishan_ont	Chromosome	55,939,331	140,803,543	2,461,191,119	Meishan_ont.fa.gz
Sus scrofa (pig)	Meishan	Meishan_v1	Chromosome	51,010,000	138,970,000	2,541,437,041	Meishan_v1.fa.gz
Sus scrofa (pig)	Min	Min_ont	Chromosome	53,496,842	140,064,540	2,452,651,751	Min_ont.fa.gz
Sus scrofa (pig)	Meishan	Meishan_jxau	Chromosome	16,520,000	139,170,000	2,447,357,155	MSjxau.fa.gz
Sus scrofa (pig)	Ningxiang	Ningxiang	Chromosome	26,070,000	139,030,000	2,471,468,735	NingXiang.fa.gz
Sus scrofa (pig)	Pietrain	Pietrain_hifi	Chromosome	136,198,627	139,641,192	2,648,267,759	Pietrain.fa.gz
Sus scrofa (pig)	Pietrain	Pietrain_hifi_hap1	Chromosome	102,614,721	144,525,616	2,497,225,301	Pietrain.hap1.fa.gz
Sus scrofa (pig)	Pietrain	Pietrain_hifi_hap2	Chromosome	102,516,029	145,954,575	2,588,070,121	Pietrain.hap2.fa.gz
Sus scrofa (pig)	Rongchang	Rongchang_ont	Chromosome	54,621,314	140,041,310	2,461,149,577	Rongchang_ont.fa.gz
Sus scrofa (pig)	Shawutou	Shawutou_hifi	Chromosome	99,625,942	147,165,159	2,700,194,877	Shawutou.fa.gz
Sus scrofa (pig)	Shawutou	Shawutou_hifi_hap1	Chromosome	80,756,421	145,320,757	2,584,886,178	Shawutou.hap1.fa.gz
Sus scrofa (pig)	Shawutou	Shawutou_hifi_hap2	Chromosome	98,593,389	141,717,853	2,542,795,895	Shawutou.hap2.fa.gz
Sus scrofa (pig)	Tibetan	Tibetan_hifi	Chromosome	96,739,904	146,189,145	2,657,455,228	Tibetan_hifi.fa.gz
Sus scrofa (pig)	Tibetan	Tibetan_hifi_hap1	Chromosome	72,396,874	145,920,915	2,458,119,761	Tibetan_hifi.hap1.fa.gz
Sus scrofa (pig)	Tibetan	Tibetan_hifi_hap2	Chromosome	60,697,397	145,247,221	2,416,022,152	Tibetan_hifi.hap2.fa.gz
Sus scrofa (pig)	Tibetan	Tibetan_ont	Chromosome	58,387,439	140,377,023	2,456,256,010	Tibetan_ont.fa.gz
Sus scrofa (pig)	Tongcheng	Tongcheng_clr	Chromosome	56,006,770	139,894,231	2,464,786,565	Tongcheng.fa.gz
Sus scrofa (pig)	Tunchang	Tunchang_hifi	Chromosome	90,042,475	141,927,016	2,691,421,025	Tunchang.fa.gz
Sus scrofa (pig)	Tunchang	Tunchang_hifi_hap1	Chromosome	69,848,610	141,681,052	2,600,688,391	Tunchang.hap1.fa.gz
Sus scrofa (pig)	Tunchang	Tunchang_hifi_hap2	Chromosome	69,966,989	142,759,861	2,542,088,445	Tunchang.hap2.fa.gz
Sus scrofa (pig)	Wisconsin	Wisconsinmini	Chromosome	35,546,377	140,773,172	2,517,666,472	Wisconsin.fa.gz
Sus scrofa (pig)	Wuzhishan	Wuzhishan_ont	Chromosome	51,711,424	140,170,329	2,458,859,128	Wuzhishan_ont.fa.gz
Sus scrofa (pig)	Wuzhishan	Wuzhishan_T2T	Chromosome	144,900,000	144,900,000	2,633,168,211	WuzhishanT2T.fa.gz
Sus scrofa (pig)	Largewhite	Largewhite_ont	Chromosome	57,950,283	139,313,367	2,455,078,035	Yorkshire_ont.fa.gz

 

Genus	Species/Breed	Genome name	protein_coding gene number	Nr	TrEMBL	BUSCO(mammalia_odb10)	Download link
Sus scrofa (pig)	Anqingliuwhite	Anqingliuwhite_ont	20,267	20,145	20,093	99.40%	Anqingliuwhite.complete.genomic.gtf.gz
Sus scrofa (pig)	Asianwild	Asianwild_hifi	21,175	20,710	20,605	99.60%	Asianwild.complete.genomic.gtf.gz
Sus scrofa (pig)	Babraham	Babraham_clr	20,551	20,025	19,920	99.50%	Babraham.complete.genomic.gtf.gz
Sus scrofa (pig)	Bama	Bama_hifi	21,217	20,810	20,701	99.50%	Bamahifi.complete.genomic.gtf.gz
Sus scrofa (pig)	Banna	Banna_hifi	21,397	20,680	20,570	99.60%	Banna.complete.genomic.gtf.gz
Sus scrofa (pig)	Berkshire	Berkshire_hifi	21,227	20,827	20,707	99.60%	Berkshire.complete.genomic.gtf.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet1_ont	20,900	20,476	20,375	99.60%	Berk_Tibet1.complete.genomic.gtf.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet2_ont	20,840	20,307	20,244	95.70%	Berk_Tibet2.complete.genomic.gtf.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet3_ont	20,741	20,303	20,203	99.60%	Berk_Tibet3.complete.genomic.gtf.gz
Sus scrofa (pig)	Berkshire×Tibetan	BerkTibet4_ont	20,818	20,348	20,242	99.50%	Berk_Tibet4.complete.genomic.gtf.gz
Sus scrofa (pig)	Europeanwild	Europeanwild_ont	20,296	20,044	19,964	99.40%	CentralEuropeanwild.complete.genomic.gtf.gz
Sus scrofa (pig)	Chenghua	Chenghua_hifi	21,210	20,876	20,778	99.60%	Chenghua.complete.genomic.gtf.gz
Sus scrofa (pig)	Diannanxiaoear	Diannanxiaoear_clr	21,288	20,882	20,785	99.30%	Diannanxiaoear.complete.genomic.gtf.gz
Sus scrofa (pig)	Guanzhongblack	Guanzhongblack_hifi	21,069	20,610	20,473	99.60%	Guanzhongblack.complete.genomic.gtf.gz
Sus scrofa (pig)	Hanjiangblack	Hanjiangblack_hifi	21,130	20,897	20,809	99.60%	Hanjiangblack.complete.genomic.gtf.gz
Sus scrofa (pig)	Huai	Huai_clr	20,370	20,268	20,227	99.10%	Huai.complete.genomic.gtf.gz
Sus scrofa (pig)	Jinhua	Jinhua_ont	19,951	19,930	19,931	99.50%	Jinhua_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Jinhua	jinhua_T2T	20,256	20,239	20,236	99.50%	JinhuaT2T.complete.genomic.gtf.gz
Sus scrofa (pig)	Juema	Juema_hifi	21,358	20,944	20,826	99.50%	Juema.complete.genomic.gtf.gz
Sus scrofa (pig)	Laiwu	Laiwu_clr	20,404	20,263	20,194	99.40%	Laiwu_clr.complete.genomic.gtf.gz
Sus scrofa (pig)	Laiwu	Laiwu_ont	20,364	20,210	20,144	99.50%	Laiwu_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Landrace	Landrace_hifi	20,906	20,616	20,526	99.50%	Landrace_hifi.complete.genomic.gtf.gz
Sus scrofa (pig)	Landrace	Landrace_T2T	21,143	20,733	20,630	99.60%	LandraceT2T.complete.genomic.gtf.gz
Sus scrofa (pig)	Lantang	Lantang_hifi	21,113	20,663	20,541	99.50%	Lantang.complete.genomic.gtf.gz
Sus scrofa (pig)	Largewhite	Largewhitev1_hifi	21,082	20,596	20,488	99.60%	Largewhite_hifi.complete.genomic.gtf.gz
Sus scrofa (pig)	Largewhite	Largewhitev2_hifi	21,073	20,589	20,482	99.60%	Largewhite_hifi_V2.complete.genomic.gtf.gz
Sus scrofa (pig)	Luchuan	Luchuan_clr	19,745	19,715	19,699	99.10%	Luchuan.complete.genomic.gtf.gz
Sus scrofa (pig)	Meishan	Meishan_clr	20,518	20,342	20,268	99.50%	Meishan_clr.complete.genomic.gtf.gz
Sus scrofa (pig)	Meishan	Meishan_ont	20,798	20,407	20,293	99.60%	Meishan_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Meishan	Meishan_v1	20,734	20,406	20,302	99.50%	Meishan_v1.complete.genomic.gtf.gz
Sus scrofa (pig)	Min	Min_ont	20,283	20,173	20,111	99.60%	Min_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Meishan	Meishan_jxau	20,475	20,085	19,964	99.60%	MSjxau.complete.genomic.gtf.gz
Sus scrofa (pig)	Ningxiang	Ningxiang	19,989	19,904	19,881	99.50%	Ningxiang.complete.genomic.gtf.gz
Sus scrofa (pig)	Pietrain	Pietrain_hifi	21,650	20,921	20,790	99.50%	Pietrain.complete.genomic.gtf.gz
Sus scrofa (pig)	Rongchang	Rongchang_ont	20,806	20,391	20,278	99.60%	Rongchang_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Shawutou	Shawutou_hifi	21,057	20,668	20,547	99.60%	Shawutou.complete.genomic.gtf.gz
Sus scrofa (pig)	Tibetan	Tibetan_hifi	20,496	20,402	20,349	99.60%	Tibetan_hifi.complete.genomic.gtf.gz
Sus scrofa (pig)	Tibetan	Tibetan_ont	20,272	20,160	20,112	99.50%	Tibetan_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Tongcheng	Tongcheng_clr	21,228	20,648	20,528	99.60%	Tongcheng.complete.genomic.gtf.gz
Sus scrofa (pig)	Tunchang	Tunchang_hifi	21,440	20,849	20,728	99.50%	Tunchang.complete.genomic.gtf.gz
Sus scrofa (pig)	Wisconsin	Wisconsinmini	20,717	20,221	20,108	99.00%	Wisconsin.complete.genomic.gtf.gz
Sus scrofa (pig)	Wuzhishan	Wuzhishan_ont	21,034	20,421	20,310	99.60%	Wuzhishan_ont.complete.genomic.gtf.gz
Sus scrofa (pig)	Wuzhishan	Wuzhishan_T2T	21,471	20,862	20,754	99.60%	WuzhishanT2T.complete.genomic.gtf.gz
Sus scrofa (pig)	Largewhite	Largewhite_ont	20,773	20,286	20,175	99.60%	Yorkshire_ont.complete.genomic.gtf.gz