一文读懂参考基因组和基因组注释+最全下载方法

白墨石

发布于 2021-06-10 10:02:37

2.8K0

发布于 2021-06-10 10:02:37

文章被收录于专栏：生信情报站

一、什么是参考基因组和基因组注释？

先来理一理参考基因组，基因组注释文件间的关系。

自从 1990 启动的家喻户晓的人类基因组计划开始，全世界的科学家竭尽全力破译了第一个完整的人类基因组，从那时开始人类拿到了一本只有 ATCG 四个碱基书写的天书。后续人们逐步完善了基因组序列信息，并写在 Fasta 格式的文本文件“天书”中，这本天书就叫做参考基因组。

但是，直接拿天书来看是一脸懵逼的，于是大家开始利用实验技术手段开始着手解密这本天书，随后大量的基因以及非编码序列被人们详细的标记在参考基因组对应的位置。同时对该位置加入大量的注释细节，最终将这些信息写在 BED，GTF，GFF 格式的基因组注释文件。所以也可以把基因组注释文件理解为字典，看不懂天书，翻翻字典就懂了。

随着时间的推移，在更先进技术的加持下，在已经构建好的基因组和注释信息上不断增加，删减，修改，就有了不同的版本。而每一个版本的参考基因组都会对应有一个基因组注释文件（天书和字典一一对应），接下来我们看看参考基因组版本是怎么指定的。

二、参考基因组版本命名

在讲参考基因组之前，需要提到一个组织参考基因组联盟（Genome Reference Consortium），它是由 NCBI，EBI，桑格研究所等机构组成。GRC 利用最佳的技术装配，纠正，增加基因组序列，以此作为在生信分析领域作为参考的基因组。目前，该机构构建了人，小鼠，大鼠，斑马鱼，鸡的参考基因组。

人基因组官名叫 GRCh38 （Genome Reference Consortium Human Build 38），GRCh38 在UCSC基因组浏览器中还有个小名 hg38，这个小名对于大多数人来说是更亲切熟悉的。GRCh38 在 GenBank 中叫 GCA_000001405.15，在 RefSeq 中叫 GCF_000001405.26，虽然 GRC 组织建议在所有出版物和工具中使用该编号，但事实是前两种 GRCh38 和 hg38 对生信分析更常见。

在不更改染色体坐标的情况下，向参考基因组添加或替换新序列，这种打补丁的方式，会在基因组版本后加 .p （patch）来命名。

这就像在王者荣耀，英雄联盟中，为了维持游戏热度，会大幅修改游戏架构，流程，世界观，图片，叫大版本更新，而定期对某些英雄的面板属性修正，作为补丁。

举个例子，GRCh38 的第九个补丁，正式版本叫做 Genome Reference Consortium Human Build 38 patch release 9，简称 GRCh38.p9。在 GenBank 编号为 GCA_000001405.24，RefSeq 编号为 GCF_000001405.35。在 Ensemble 编号为 GRCh38，NCBI 编号为 GRCh38。

1、常用人参考基因组对应表

发布时间	2013	2009	2006
GRC 官名	GRCh38	GRCh37	GRCh36
UCSC	hg38	hg19	hg18
Ensemble	GRCh38	GRCh37	GRCh36
GENCODE	38	19	3c
NCBI	GRCh38	GRCh37	GRCh36
GenBank	GCA_000001405
RefSeq	GCF_000001405

根据 GRC 官网信息，GRCh39 大版本将会无限停更，他们在考虑用新模型和序列来构建人类的参考基因组，细节不清楚，猜测有可能会有泛基因组内容。

2、常用小鼠参考基因组对应表

发布时间	2020	2011	2007
GRC 官名	GRCm39	GRCm38
UCSC	m39	mm10	mm9
Ensemble	GRCm39	GRCm38
GENCODE	M27	M25	M1
NCBI	GRCm39	GRCm38	NCBIM37

三、下载

1、NCBI

这里提供两种下载方式，一种为网页界面下载，另一种为FTP下载。

可视化下载

进入网址

https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/

搜索物种

下载界面

FTP下载

随便提一下，Chrome 浏览器在18版本后由于安全原因已经不支持 ftp 协议，改用 https 协议，可以看到链接已经与之前的不同。

这里以下载人的参考基因组 GRCh38 为例：

https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference/GCF_000001405.39_GRCh38.p13

人类基因组注释文件：

GTF 格式：https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/109/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gtf.gz

GFF 格式：

https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/109/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz

如果以这种方式下载，其实已经可以路径中大概看出相关物种的下载地址，可以自行查询及下载其他物种。

2、Ensemble

可视化下载

网址：http://asia.ensembl.org
点击物种名，进入下载界面

点击对应名称，下载参考基因组和基因组注释文件

FTP下载

同样以下载人参考基因组 GRCh38 为例：

http://ftp.ensembl.org/pub/current_fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz

GTF 文件：http://ftp.ensembl.org/pub/current_gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz

GTT 文件：http://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz

3、GENCODE

如果小伙伴研究的物种只涉及人类和小鼠，极力推荐 GENCOE，这里有着相较其他数据库，最新最全的基因组和其注释信息。

网址：https://www.gencodegenes.org/
点击人类的最新版

点击下载基因组注释文件

点击下载参考基因组文件

4、UCSC

相对其他下载方式，UCSC 本职的工作是做基因组浏览器的，因此也可以从下图看到，在这里可以根据自己定义来下载相对于的基因组区域，比如 prime，exon，gene，transcript等等。

网址：http://genome.ucsc.edu/cgi-bin/hgTables
下载：设置参数如下，然后点击下载参考基因组及注释文件

5、iGenomes

iGenomes是常见分析生物的参考序列和注释文件的集合。这些文件已从Ensembl，NCBI或UCSC下载。染色体名称已更改为简单且与下载源一致。每个iGenome都可以作为压缩文件使用，其中包含生物体的单个基因组构建的序列和注释文件。

网址：https://support.illumina.com/sequencing/sequencing_software/igenome.html

由亚马逊资助的生物信息参考基因组下载站点，有各种参考基因组，注释文件，软件索引等常用文件，并且有着极快的下载速度，但是缺点是只有常用的物种。

**站点：**https://ewels.github.io/AWS-iGenomes/

四、其他参考基因组信息

SPECIES	UCSC VERSION	RELEASE DATE	RELEASE NAME	STATUS
MAMMALS
Human	hg38	Dec. 2013	Genome Reference Consortium GRCh38	Available
	hg19	Feb. 2009	Genome Reference Consortium GRCh37	Available
	hg18	Mar. 2006	NCBI Build 36.1	Available
	hg17	May 2004	NCBI Build 35	Available
	hg16	Jul. 2003	NCBI Build 34	Available
	hg15	Apr. 2003	NCBI Build 33	Archived
	hg13	Nov. 2002	NCBI Build 31	Archived
	hg12	Jun. 2002	NCBI Build 30	Archived
	hg11	Apr. 2002	NCBI Build 29	Archived (data only)
	hg10	Dec. 2001	NCBI Build 28	Archived (data only)
	hg8	Aug. 2001	UCSC-assembled	Archived (data only)
	hg7	Apr. 2001	UCSC-assembled	Archived (data only)
	hg6	Dec. 2000	UCSC-assembled	Archived (data only)
	hg5	Oct. 2000	UCSC-assembled	Archived (data only)
	hg4	Sep. 2000	UCSC-assembled	Archived (data only)
	hg3	Jul. 2000	UCSC-assembled	Archived (data only)
	hg2	Jun. 2000	UCSC-assembled	Archived (data only)
	hg1	May 2000	UCSC-assembled	Archived (data only)
Alpaca	vicPac2	Mar. 2013	Broad Institute Vicugna_pacos-2.0.1	Available
	vicPac1	Jul. 2008	Broad Institute VicPac1.0	Available
Armadillo	dasNov3	Dec. 2011	Broad Institute DasNov3	Available
Baboon	papAnu4	Apr. 2017	Human Genome Sequencing Center	Available
	papAnu2	Mar. 2012	Baylor College of Medicine Panu_2.0	Available
	papHam1	Nov. 2008	Baylor College of Medicine HGSC Pham_1.0	Available
Bison	bisBis1	Oct. 2014	Univ. of Maryland Bison_UMD1.0	Available
Bonobo	panPan3	May 2020	University of Washington	Available
	panPan2	Dec. 2015	Max-Planck Institute for Evolutionary Anthropology panpan1.1	Available
	panPan1	May 2012	Max-Planck Institute panpan1	Available
Brown kiwi	aptMan1	Jun. 2015	Max-Planck Institute for Evolutionary Anthropology AptMant0	Available
Bushbaby	otoGar3	Mar. 2011	Broad Institute OtoGar3	Available
Cat	felCat9	Nov. 2017	Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine Felis_catus_9.0	Available
	felCat8	Nov. 2014	ICGSC Felis_catus_8.0	Available
	felCat5	Sep. 2011	ICGSC Felis_catus-6.2	Available
	felCat4	Dec. 2008	NHGRI catChrV17e	Available
	felCat3	Mar. 2006	Broad Institute Release 3	Available
Chimp	panTro6	Jan. 2018	Clint_PTRv2	Available
	panTro5	May 2016	CGSC Build 3.0	Available
	panTro4	Feb. 2011	CGSC Build 2.1.4	Available
	panTro3	Oct. 2010	CGSC Build 2.1.3	Available
	panTro2	Mar. 2006	CGSC Build 2.1	Available
	panTro1	Nov. 2003	CGSC Build 1.1	Available
Chinese hamster	criGri1	Jul. 2013	Beijing Genomics Institution-Shenzhen C_griseus_v1.0	Available
Chinese hamster ovary cell line	criGriChoV2	Jun. 2017	Eagle Genomics Ltd CHOK1S_HZDv1	Available
	criGriChoV1	Aug. 2011	Beijing Genomics Institute CriGri_1.0	Available
Chinese pangolin	manPen1	Aug. 2014	Washington University (WashU) M_pentadactyla-1.1.1	Available
Cow	bosTau9	Apr. 2018	USDA ARS	Available
	bosTau8	Jun. 2014	University of Maryland v3.1.1	Available
	bosTau7	Oct. 2011	Baylor College of Medicine HGSC Btau_4.6.1	Available
	bosTau6	Nov. 2009	University of Maryland v3.1	Available
	bosTau4	Oct. 2007	Baylor College of Medicine HGSC Btau_4.0	Available
	bosTau3	Aug. 2006	Baylor College of Medicine HGSC Btau_3.1	Available
	bosTau2	Mar. 2005	Baylor College of Medicine HGSC Btau_2.0	Available
	bosTau1	Sep. 2004	Baylor College of Medicine HGSC Btau_1.0	Archived
Crab-eating macaque	macFas5	Jun. 2013	Washington University Macaca_fascicularis_5.0	Available
Dog	canFam5	May 2019	University of Michigan	Available
	canFam4	Mar. 2020	Uppsala University	Available
	canFam3	Sep. 2011	Broad Institute v3.1	Available
	canFam2	May 2005	Broad Institute v2.0	Available
	canFam1	Jul. 2004	Broad Institute v1.0	Available
Dolphin	turTru2	Oct. 2011	Baylor College of Medicine Ttru_1.4	Available
Elephant	loxAfr3	Jul. 2009	Broad Institute LoxAfr3	Available
Ferret	musFur1	Apr. 2011	Ferret Genome Sequencing Consortium MusPutFur1.0	Available
Garter snake	thaSir1	Jun. 2015	Washington University Thamnophis_sirtalis-6.0	Available
Gibbon	nomLeu3	Oct. 2012	Gibbon Genome Sequencing Consortium Nleu3.0	Available
	nomLeu2	Jun. 2011	Gibbon Genome Sequencing Consortium Nleu1.1	Available
	nomLeu1	Jan. 2010	Gibbon Genome Sequencing Consortium Nleu1.0	Available
Golden eagle	aquChr2	Oct. 2014	University of Washington aquChr2-1.0.2	Available
Golden snub-nosed monkey	rhiRox1	Oct. 2014	Novogene Rrox_v1	Available
Gorilla	gorGor6	Aug. 2019	University of Washington	Available
	gorGor5	Mar. 2016	University of Washington GSMRT3	Available
	gorGor4	Dec. 2014	Wellcome Trust Sanger Institute gorGor4	Available
	gorGor3	May 2011	Wellcome Trust Sanger Institute gorGor3.1	Available
Green Monkey	chlSab2	Mar. 2014	Vervet Genomics Consortium 1.1	Available
Guinea pig	cavPor3	Feb. 2008	Broad Institute cavPor3	Available
Hawaiian monk seal	neoSch1	Jun. 2017	Johns Hopkins University ASM220157v1	Available
Hedgehog	eriEur2	May 2012	Broad Institute EriEur2.0	Available
	eriEur1	Jun. 2006	Broad Institute Draft_v1	Available
Horse	equCab3	Jan. 2018	University of Louisville	Available
	equCab2	Sep. 2007	Broad Institute EquCab2	Available
	equCab1	Jan. 2007	Broad Institute EquCab1	Available
Kangaroo rat	dipOrd1	Jul. 2008	Baylor/Broad Institute DipOrd1.0	Available
Malayan flying lemur	galVar1	Jul. 2014	WashU G_variegatus-3.0.2	Available
Manatee	triMan1	Oct. 2011	Broad Institute TriManLat1.0	Available
Marmoset	calJac4	May 2020	Washington University Callithrix_jacchus_cj1700_1.1	Available
Marmoset	calJac3	Mar. 2009	WUSTL Callithrix_jacchus-v3.2	Available
	calJac1	Jun. 2007	WUSTL Callithrix_jacchus-v2.0.2	Available
Megabat	pteVam1	Jul. 2008	Broad Institute Ptevap1.0	Available
Microbat	myoLuc2	Jul. 2010	Broad Institute MyoLuc2.0	Available
Minke whale	balAcu1	Oct. 2013	KORDI BalAcu1.0	Available
Mouse	mm39	Jun. 2020	Genome Reference Consortium Mouse Build 39	Available
	mm10	Dec. 2011	Genome Reference Consortium GRCm38	Available
	mm9	Jul. 2007	NCBI Build 37	Available
	mm8	Feb. 2006	NCBI Build 36	Available
	mm7	Aug. 2005	NCBI Build 35	Available
	mm6	Mar. 2005	NCBI Build 34	Archived
	mm5	May 2004	NCBI Build 33	Archived
	mm4	Oct. 2003	NCBI Build 32	Archived
	mm3	Feb. 2003	NCBI Build 30	Archived
	mm2	Feb. 2002	MGSCv3	Archived
	mm1	Nov. 2001	MGSCv2	Archived (data only)
Mouse lemur	micMur2	May 2015	Baylor/Broad Institute Mmur_2.0	Available
	micMur1	Jul. 2007	Broad Institute MicMur1.0	Available
Naked mole-rat	hetGla2	Jan. 2012	Broad Institute HetGla_female_1.0	Available
	hetGla1	Jul. 2011	Beijing Genomics Institute HetGla_1.0	Available
Opossum	monDom5	Oct. 2006	Broad Institute release MonDom5	Available
	monDom4	Jan. 2006	Broad Institute release MonDom4	Available
	monDom1	Oct. 2004	Broad Institute release MonDom1	Available
Orangutan	ponAbe2	Jul. 2007	WUSTL Pongo_albelii-2.0.2	Available
	ponAbe3	Jan. 2018	Susie_PABv2/ponAbe3	Available
Panda	ailMel1	Dec. 2009	BGI-Shenzhen AilMel 1.0	Available
Pig	susScr11	Feb. 2017	Swine Genome Sequencing Consortium Sscrofa11.1	Available
	susScr3	Aug. 2011	Swine Genome Sequencing Consortium Sscrofa10.2	Available
	susScr2	Nov. 2009	Swine Genome Sequencing Consortium Sscrofa9.2	Available
Pika	ochPri3	May 2012	Broad Institute OchPri3.0	Available
	ochPri2	Jul. 2008	Broad Institute OchPri2	Available
Platypus	ornAna2	Feb. 2007	WUSTL v5.0.1	Available
	ornAna1	Mar. 2007	WUSTL v5.0.1	Available
Proboscis Monkey	nasLar1	Nov. 2014	Proboscis Monkey Functional Genome Consortium Charlie1.0	Available
Rabbit	oryCun2	Apr. 2009	Broad Institute release OryCun2	Available
Rat	rn7	Nov. 2020	Wellcome Sanger Institute mRatBN7.2	Available
	rn6	Jul. 2014	RGSC Rnor_6.0	Available
	rn5	Mar. 2012	RGSC Rnor_5.0	Available
	rn4	Nov. 2004	Baylor College of Medicine HGSC v3.4	Available
	rn3	Jun. 2003	Baylor College of Medicine HGSC v3.1	Available
	rn2	Jan. 2003	Baylor College of Medicine HGSC v2.1	Archived
	rn1	Nov. 2002	Baylor College of Medicine HGSC v1.0	Archived
Rhesus	rheMac10	Feb. 2019	The Genome Institute at Washington University School of Medicine Mmul_10	Available
	rheMac8	Nov. 2015	Baylor College of Medicine HGSC Mmul_8.0.1	Available
	rheMac3	Oct. 2010	Beijing Genomics Institute CR_1.0	Available
	rheMac2	Jan. 2006	Baylor College of Medicine HGSC v1.0 Mmul_051212	Available
	rheMac1	Jan. 2005	Baylor College of Medicine HGSC Mmul_0.1	Archived
Rock hyrax	proCap1	Jul. 2008	Baylor College of Medicine HGSC Procap1.0	Available
Sheep	oviAri4	Dec. 2015	ISGC Oar_v4.0	Available
	oviAri3	Aug. 2012	ISGC Oar_v3.1	Available
	oviAri1	Feb. 2010	ISGC Ovis aries 1.0	Available
Shrew	sorAra2	Aug. 2008	Broad Institute SorAra2.0	Available
	sorAra1	Jun. 2006	Broad Institute SorAra1.0	Available
Sloth	choHof1	Jul. 2008	Broad Institute ChoHof1.0	Available
Squirrel	speTri2	Nov. 2011	Broad Institute SpeTri2.0	Available
Squirrel monkey	saiBol1	Oct. 2011	Broad Institute SaiBol1.0	Available
Tarsier	tarSyr2	Sep. 2013	WashU Tarsius_syrichta-2.0.1	Available
	tarSyr1	Aug. 2008	WUSTL/Broad Institute Tarsyr1.0	Available
Tasmanian devil	sarHar1	Feb. 2011	Wellcome Trust Sanger Institute Devil_refv7.0	Available
Tenrec	echTel2	Nov. 2012	Broad Institute EchTel2.0	Available
	echTel1	Jul. 2005	Broad Institute echTel1	Available
Tree shrew	tupBel1	Dec. 2006	Broad Institute Tupbel1.0	Available
Wallaby	macEug2	Sep. 2009	Tammar Wallaby Genome Sequencing Consortium Meug_1.1	Available
White rhinoceros	cerSim1	May 2012	Broad Institute CerSimSim1.0	Available

VERTEBRATES
African clawed frog	xenLae2	Aug. 2016	Int. Xenopus Sequencing Consortium	Available
American alligator	allMis1	Aug. 2012	Int. Crocodilian Genomes Working Group allMis0.2	Available
Atlantic cod	gadMor1	May 2010	Genofisk GadMor_May2010	Available
Budgerigar	melUnd1	Sep. 2011	WUSTL v6.3	Available
Chicken	galGal6	Mar. 2018	GRCg6 Gallus-gallus-6.0	Available
	galGal5	Dec. 2015	ICGC Gallus-gallus-5.0	Available
	galGal4	Nov. 2011	ICGC Gallus-gallus-4.0	Available
	galGal3	May 2006	WUSTL Gallus-gallus-2.1	Available
	galGal2	Feb. 2004	WUSTL Gallus-gallus-1.0	Available
Coelacanth	latCha1	Aug. 2011	Broad Institute LatCha1	Available
Elephant shark	calMil1	Dec. 2013	IMCB Callorhinchus_milli_6.1.3	Available
Fugu	fr3	Oct. 2011	JGI v5.0	Available
	fr2	Oct. 2004	JGI v4.0	Available
	fr1	Aug. 2002	JGI v3.0	Available
Lamprey	petMar3	Dec. 2017	University of Kentucky Pmar_germline 1.0	Available
	petMar2	Sep. 2010	WUGSC 7.0	Available
	petMar1	Mar. 2007	WUSTL v3.0	Available
Lizard	anoCar2	May 2010	Broad Institute AnoCar2	Available
	anoCar1	Feb. 2007	Broad Institute AnoCar1	Available
Medaka	oryLat2	Oct. 2005	NIG v1.0	Available
Medium ground finch	geoFor1	Apr. 2012	BGI GeoFor_1.0 / NCBI 13302	Available
Nile tilapia	oreNil2	Jan. 2011	Broad Institute Release OreNil1.1	Available
Painted turtle	chrPic1	Dec. 2011	IPTGSC Chrysemys_picta_bellii-3.0.1	Available
Stickleback	gasAcu1	Feb. 2006	Broad Institute Release 1.0	Available
Tetraodon	tetNig2	Mar. 2007	Genoscope v7	Available
	tetNig1	Feb. 2004	Genoscope v7	Available
Tibetan frog	nanPar1	Mar. 2015	Beijing Genomics Institute BGI_ZX_20015	Available
Turkey	melGal5	Nov. 2014	Turkey Genome Consortium v5.0	Available
	melGal1	Dec. 2009	Turkey Genome Consortium v2.01	Available
X. tropicalis	xenTro9	Jul. 2016	JGI v.9.1	Available
	xenTro7	Sep. 2012	JGI v.7.0	Available
	xenTro3	Nov. 2009	JGI v.4.2	Available
	xenTro2	Aug. 2005	JGI v.4.1	Available
	xenTro1	Oct. 2004	JGI v.3.0	Available
Zebra finch	taeGut2	Feb. 2013	WashU taeGut324	Available
	taeGut1	Jul. 2008	WUSTL v3.2.4	Available
Zebrafish	danRer11	May 2017	Genome Reference Consortium GRCz11	Available
	danRer10	Sep. 2014	Genome Reference Consortium GRCz10	Available
	danRer7	Jul. 2010	Sanger Institute Zv9	Available
	danRer6	Dec. 2008	Sanger Institute Zv8	Available
	danRer5	Jul. 2007	Sanger Institute Zv7	Available
	danRer4	Mar. 2006	Sanger Institute Zv6	Available
	danRer3	May 2005	Sanger Institute Zv5	Available
	danRer2	Jun. 2004	Sanger Institute Zv4	Archived
	danRer1	Nov. 2003	Sanger Institute Zv3	Archived

DEUTEROSTOMES
C. intestinalis	ci3	Apr. 2011	Kyoto KH	Available
C. intestinalis	ci2	Mar. 2005	JGI v2.0	Available
	ci1	Dec. 2002	JGI v1.0	Available
Lancelet	braFlo1	Mar. 2006	JGI v1.0	Available
S. purpuratus	strPur2	Sep. 2006	Baylor College of Medicine HGSC v. Spur 2.1	Available
	strPur1	Apr. 2005	Baylor College of Medicine HGSC v. Spur_0.5	Available

INSECTS
A. mellifera	apiMel2	Jan. 2005	Baylor College of Medicine HGSC v.Amel_2.0	Available
	apiMel1	Jul. 2004	Baylor College of Medicine HGSC v.Amel_1.2	Available
A. gambiae	anoGam3	Oct. 2006	International Consortium for the Sequencing of Anopheles Genome AgamP3	Available
	anoGam1	Feb. 2003	IAGP v.MOZ2	Available
D. ananassae	droAna2	Aug. 2005	Agencourt Arachne release	Available
	droAna1	Jul. 2004	TIGR Celera release	Available
D. erecta	droEre1	Aug. 2005	Agencourt Arachne release	Available
D. grimshawi	droGri1	Aug. 2005	Agencourt Arachne release	Available
D. melanogaster	dm6	Aug. 2014	BDGP Release 6 + ISO1 MT	Available
	dm3	Apr. 2006	BDGP Release 5	Available
	dm2	Apr. 2004	BDGP Release 4	Available
	dm1	Jan. 2003	BDGP Release 3	Available
D. mojavensis	droMoj2	Aug. 2005	Agencourt Arachne release	Available
	droMoj1	Aug. 2004	Agencourt Arachne release	Available
D. persimilis	droPer1	Oct. 2005	Broad Institute release	Available
D. pseudoobscura	dp3	Nov. 2004	FlyBase Release 1.0	Available
	dp2	Aug. 2003	Baylor College of Medicine HGSC Freeze 1	Available
D. sechellia	droSec1	Oct. 2005	Broad Institute Release 1.0	Available
D. simulans	droSim1	Apr. 2005	WUSTL Release 1.0	Available
D. virilis	droVir2	Aug. 2005	Agencourt Arachne release	Available
	droVir1	Jul. 2004	Agencourt Arachne release	Available
D. yakuba	droYak2	Nov. 2005	WUSTL Release 2.0	Available
	droYak1	Apr. 2004	WUSTL Release 1.0	Available

NEMATODES
C. brenneri	caePb2	Feb. 2008	WUSTL 6.0.1	Available
	caePb1	Jan. 2007	WUSTL 4.0	Available
C. briggsae	cb3	Jan. 2007	WUSTL Cb3	Available
	cb1	Jul. 2002	WormBase v. cb25.agp8	Available
C. elegans	ce11	Feb. 2013	C. elegans Sequencing Consortium WBcel235	Available
	ce10	Oct. 2010	WormBase v. WS220	Available
	ce6	May 2008	WormBase v. WS190	Available
	ce4	Jan. 2007	WormBase v. WS170	Available
	ce2	Mar. 2004	WormBase v. WS120	Available
	ce1	May 2003	WormBase v. WS100	Archived
C. japonica	caeJap1	Mar. 2008	WUSTL 3.0.2	Available
C. remanei	caeRem3	May 2007	WUSTL 15.0.1	Available
	caeRem2	Mar. 2006	WUSTL 1.0	Available
P. pacificus	priPac1	Feb. 2007	WUSTL 5.0	Available

OTHER
Sea Hare	aplCal1	Sep. 2008	Broad Release Aplcal2.0	Available
Yeast	sacCer3	April 2011	SGD April 2011 sequence	Available
	sacCer2	June 2008	SGD June 2008 sequence	Available
	sacCer1	Oct. 2003	SGD 1 Oct 2003 sequence	Available

VIRUSES
Ebola Virus	eboVir3	June 2014	Sierra Leone 2014 (G3683/KM034562.1)	Available
SARS-CoV-2	wuhCor1	Jan. 2020	SARS-CoV-2 ASM985889v3	Available