新型冠状病毒信息库 UCloud本地镜像

本次公布的全量病毒、人类病例基因组数据是11GB左右,因为都在美国NCBI 库,访问下载只有10KB/S左右。 UCloud同事自发把这些数据全量都拉到ufile上。这样,国内的药研、科研要用直接下载,速度会快很多。

#说明

2019新型冠状病毒信息库(本库由中国国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建设),针对本次2019-nCoV新型冠状病毒,自2020年1月20日起,由国家生物信息中心维护并公开病毒基因序列库(https://bigd.big.ac.cn/ncov#

其中,截止至2020年1月31日14时,共计累计基因序列67份,其中最重要的病毒基因核对样本MN908947,目前已于1月23日维护更新至第三版本(MN908947.3,获取地址:http://2019ncov-gene.ucloud365.com/2019-ncov/MN908947/MN908947.3.txt

本病毒基因序列,可用于:

  • 通过高通量测序法,确定患者是否感染2019-nCoV新型冠状病毒,用于医学确诊。

  • 医学研究,用于研制临床药物、用于分析病毒株基因组成

  • 药物试验,疗程比对

  • 科学研究、生物药研制

  • 等等

目前所有病例序列均已镜像至UCloud UFile地址:http://2019ncov-gene.ucloud365.com/路径下,详见下表。

另包含6分完整人类RNA-seq序列(SRA序列),用于分析Coronavirinae、Bat SARS-like coronavirus、SARS coronavirus病毒与其他细胞、菌类、病毒在人体中的结合反应。

img

因SRA序列位于美国NCBI,且数据量大、传输时间久等不便性原因,目前已将截止至目前的2019-nCoV所有的SRA序列同步保持在UCloud Ufile公共服务中,可在国内无损访问。

目前SRA提供列表(对应下载路径见下表):

SRA Run BioProject BioSample
SRR10903401 PRJNA601736 SAMN13872787
SRR10903402 PRJNA601736 SAMN13872786
SRR10902284 PRJNA601630 SAMN13871323
SRR10948474 PRJNA601630 SAMN13898864
SRR10948550 PRJNA601630 SAMN13871323
SRR10971381 PRJNA603194 SAMN13922059

可提供格式:

  • run格式

  • fastq格式

# 使用方法

内网算力使用纪要测序数据【更快】

使用UCloud算力做生物科研计算时,可通过内网获取以上病毒基因序列、SRA基因序列。

使用内网域名前缀:http://2019ncov.ufile.cn-north-02.ucloud.cn/

例如:SRR10971381 【约2.6GB】

公网访问:http://2019ncov-gene.ucloud365.com//data/SRR10971381/SRR10971381【传输速度取决于互联网接入带宽】

内网访问:Windows Server或Linux均可

使用内网前缀http://2019ncov.ufile.cn-north-02.ucloud.cn/替换公网域名前缀http://2019ncov-gene.ucloud365.com/

文件名保持不变,仍为“/data/SRR10971381/SRR10971381

构成内网访问完整域名:

http://2019ncov.ufile.cn-north-02.ucloud.cn//data/SRR10971381/SRR10971381

访问下载速度,可达50MB/S

img

病毒基因/SRA基因-开放数据获取链接

#武汉新型冠状病毒,完整6人的SRA数据(总共10,576MB)

.

├── SRR10902284

│ ├── HKU-SZ-002a.fastq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10902284/HKU-SZ-002a.fastq

│ └── SRR10902284 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10902284/SRR10902284

├── SRR10903401

│ ├── SRR10903401 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903401/SRR10903401

│ ├── wuhan2_1.fq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903401/wuhan2_1.fq

│ └── wuhan2_2.fq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903401/wuhan2_2.fq

├── SRR10903402

│ ├── SRR10903402 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903402/SRR10903402

│ ├── wuhan1_1.fq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903402/wuhan1_1.fq

│ └── wuhan1_2.fq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10903402/wuhan1_2.fq

├── SRR10948474

│ ├── HKU-SZ-005b.fastq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10948474/HKU-SZ-005b.fastq

│ └── SRR10948474 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10948474/SRR10948474

├── SRR10948550

│ ├── HKU-SZ-002a.fastq 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10948550/HKU-SZ-002a.fastq

│ └── SRR10948550 下载链接【http://2019ncov-gene.ucloud365.com//data/SRR10948550/SRR10948550

└── SRR10971381

├── SRR10971381    下载链接【<http://2019ncov-gene.ucloud365.com//data/SRR10971381/SRR10971381>】 

├── WH_R1.fastq.gz    下载链接【<http://2019ncov-gene.ucloud365.com//data/SRR10971381/WH_R1.fastq.gz>】 

└── WH_R2.fastq.gz    下载链接【<http://2019ncov-gene.ucloud365.com//data/SRR10971381/WH_R2.fastq.gz>】 

MD5值

111aa01b968a29694759905586c9bb08 SRR10902284/HKU-SZ-002a.fastq

67992d0e956586b36203b420e792c624 SRR10902284/SRR10902284

7dbb0781706958c5a41bdfe00c0d3139 SRR10903401/SRR10903401

fb937b54ca7660798e59d956c20726d1 SRR10903401/wuhan2_1.fq

18ca6788e0743724950b2f84e5381b15 SRR10903401/wuhan2_2.fq

20185a16203fac820c6aff8c43551163 SRR10903402/SRR10903402

59a047a121fd386480b951298402c8bf SRR10903402/wuhan1_1.fq

e9421e27a34520c440b1406a8935b3fd SRR10903402/wuhan1_2.fq

a4329bede84fb25ef18e962429183426 SRR10948474/HKU-SZ-005b.fastq

49a7987cf89ec4b8be385f5d213f6515 SRR10948474/SRR10948474

4e3884437bfac446307faea9c8ca5204 SRR10948550/HKU-SZ-002a.fastq

2377d422be45d82de70a972d3dac6d70 SRR10948550/SRR10948550

5496488662893a836e23541b84bfb7cd SRR10971381/SRR10971381

60b05398282866f57ecfb7e39916564b SRR10971381/WH_R1.fastq.gz

57ac2276c47b4000b42b06d97267ed3c SRR10971381/WH_R2.fastq.gz

SHA256值

e19e4745ed7b83907a41e5e11ebf58918caa3d986a0c56b1daaeaad4b41fbf6a SRR10902284/HKU-SZ-002a.fastq

dfc44beef6db122909665f41457ce757293a656c5758806d1e228814f297ffa6 SRR10902284/SRR10902284

91a7036abf2d0e4f8419d4106d26e6f623f5c1c0d9919b2c8aa7681f90f488fb SRR10903401/SRR10903401

038b652f07178113e54d2b25d8ca7d23773345b3148c0dfea2e64ea26d312d50 SRR10903401/wuhan2_1.fq

022b12c7f8d1b3b8afb6f978277fe9131e5e8a70eede6067a374547cc64214ba SRR10903401/wuhan2_2.fq

178b48b24fb72b9821da93de50adf4736ad5dfed2e7713c722ddd88089cd1c00 SRR10903402/SRR10903402

af7a7e551823a987dde36739d6cdc329149d4ecdbd7b1095b260be7e5c42cbca SRR10903402/wuhan1_1.fq

44bd5d00812967067305cf2d2786b47db45b4c8eb09517cc5962440409065e5a SRR10903402/wuhan1_2.fq

39d2a38acf761e5fbfc2c56115cc38b93dfdcc68d5c9e47bc7f6f0404702a5fa SRR10948474/HKU-SZ-005b.fastq

425a155ef4ce5224e347b0d4c1428a75bd421d768b7226fcdae1ef372fbc9e22 SRR10948474/SRR10948474

f81d5ba4bad06dfad4191d1d3293a4ee4a5a8df14ae04bbabf57c07aa994915b SRR10948550/HKU-SZ-002a.fastq

c53303c5567f8e5b2622f4a1f1169a47a5ed8702be5246ce67acef4b325f5b1f SRR10948550/SRR10948550

6ffe8f4890b7b51f2984bd084e36ce0ce4f0b69b9f992a5818efcb08e1f9f007 SRR10971381/SRR10971381

e2b55f2900da7dea75bb9f03ad060bc88917bc498a89fcfa06a1d2334c354355 SRR10971381/WH_R1.fastq.gz

fc8100422cd89b6525e743a5957e0c63f7191eff52a029b52b03072eab2e51bb SRR10971381/WH_R2.fastq.gz

#NCBI病毒基因序列文件【目前共计29份独立样本】

.

├── MN908947

│ ├── MN908947.3.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN908947/MN908947.3.txt

│ └── NC_045512.2.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN908947/NC_045512.2.txt

├── MN938384

│ └── MN938384.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938384/MN938384.txt

├── MN938385.1

│ └── MN938385.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938385.1/MN938385.1.txt

├── MN938386.1

│ └── MN938386.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938386.1/MN938386.1.txt

├── MN938387.1

│ └── MN938387.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938387.1/MN938387.1.txt

├── MN938388.1

│ └── MN938388.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938388.1/MN938388.1.txt

├── MN938389.1

│ └── MN938389.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938389.1/MN938389.1.txt

├── MN938390.1

│ └── MN938390.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN938390.1/MN938390.1.txt

├── MN970003.1

│ └── MN970003.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN970003.1/MN970003.1.txt

├── MN970004.1

│ └── MN970004.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN970004.1/MN970004.1.txt

├── MN975262.1

│ └── MN975262.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975262.1/MN975262.1.txt

├── MN975263.1

│ └── MN975263.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975263.1/MN975263.1.txt

├── MN975264.1

│ └── MN975264.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975264.1/MN975264.1.txt

├── MN975265.1

│ └── MN975265.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975265.1/MN975265.1.txt

├── MN975266.1

│ └── MN975266.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975266.1/MN975266.1.txt

├── MN975267.1

│ └── MN975267.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975267.1/MN975267.1.txt

├── MN975268.1

│ └── MN975268.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN975268.1/MN975268.1.txt

├── MN985325.1

│ └── MN985325.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN985325.1/MN985325.1.txt

├── MN988668.1

│ └── MN988668.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN988668.1/MN988668.1.txt

├── MN988669.1

│ └── MN988669.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN988669.1/MN988669.1.txt

├── MN988713.1

│ └── MN988713.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN988713.1/MN988713.1.txt

├── MN994467.1

│ └── MN994467.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN994467.1/MN994467.1.txt

├── MN994468.1

│ └── MN994468.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN994468.1/MN994468.1.txt

├── MN996527.1

│ └── MN996527.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN996527.1/MN996527.1.txt

├── MN996528.1

│ └── MN996528.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN996528.1/MN996528.1.txt

├── MN996529.1

│ └── MN996529.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN996529.1/MN996529.1.txt

├── MN996530.1

│ └── MN996530.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN996530.1/MN996530.1.txt

├── MN996531.1

│ └── MN996531.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN996531.1/MN996531.1.txt

├── MN997409.1

│ └── MN997409.1.txt 下载链接【http://2019ncov-gene.ucloud365.com/2019-ncov/MN997409.1/MN997409.1.txt

MD5值

MD5 (MN908947/MN908947.3.txt) = c82746de0092a64dd444dbf2757c8aee

MD5 (MN908947/NC_045512.2.txt) = b1f6176af52489b7f9da404d61433a3f

MD5 (MN938384/MN938384.txt) = 791d284e10405b98f6b429bae6a5dde1

MD5 (MN938385.1/MN938385.1.txt) = 8e7ebd98a38c3c26e8f3e7a26dd605c3

MD5 (MN938386.1/MN938386.1.txt) = 37450ca817395c5d7cda53dd97e8e012

MD5 (MN938387.1/MN938387.1.txt) = b5cc575b244f2f4b35e6afbc5049c288

MD5 (MN938388.1/MN938388.1.txt) = ec9e28909b303f8267822f7b6c3573f7

MD5 (MN938389.1/MN938389.1.txt) = 59285bc40877d946cc9d841d867c26c6

MD5 (MN938390.1/MN938390.1.txt) = 1fb33fb583b5f7977ac28059a03ac0de

MD5 (MN970003.1/MN970003.1.txt) = 3098ec0672595c163785de255c71355b

MD5 (MN970004.1/MN970004.1.txt) = 529a921e5013f4816033ed9ae42406ae

MD5 (MN975262.1/MN975262.1.txt) = f2df286a75a2a6e56f8a1b567197db59

MD5 (MN975263.1/MN975263.1.txt) = 417d76b823268a2f7f1c75bcc037bdca

MD5 (MN975264.1/MN975264.1.txt) = 008f2a08239eafee6cd1619f5d958f9c

MD5 (MN975265.1/MN975265.1.txt) = 6cb4dbab620b64b37d3bc398d6da1c96

MD5 (MN975266.1/MN975266.1.txt) = be2e90a5d8c0baa134eae7825d3fcd38

MD5 (MN975267.1/MN975267.1.txt) = 86725e2966efea90c54fdf23ccd65f2d

MD5 (MN975268.1/MN975268.1.txt) = 4358cc5520fedd098bc6ca9f7e30e7a1

MD5 (MN985325.1/MN985325.1.txt) = 1dd9b96f1f3f1b88cc6933f8d6eca2fa

MD5 (MN988668.1/MN988668.1.txt) = 733a472624aa1415abdf68e0792fcf77

MD5 (MN988669.1/MN988669.1.txt) = 974970bd04041e34da1b7d60b37b3a12

MD5 (MN988713.1/MN988713.1.txt) = 21fe02058d650613ca04e03a6a13079e

MD5 (MN994467.1/MN994467.1.txt) = 65df610560ef73e2c97844f8a961ac1a

MD5 (MN994468.1/MN994468.1.txt) = 456ba3d4a87fd041c82dc922497e8026

MD5 (MN996527.1/MN996527.1.txt) = af986defc07c92046cb978d3bb43da1c

MD5 (MN996528.1/MN996528.1.txt) = b726c2d6cc9db2a9df8ef118b697f775

MD5 (MN996529.1/MN996529.1.txt) = 6edddb3f1e43a12169c3a534ef03390a

MD5 (MN996530.1/MN996530.1.txt) = 7665c2d0288a02ffac7ca73cd125ff8b

MD5 (MN996531.1/MN996531.1.txt) = 39186b5bb000f867547cffedfdeb7cc9

MD5 (MN997409.1/MN997409.1.txt) = 3bd70773c61d760694399cdfad35d59b

SHA256值

c4305cb934bea663ed5d4f6b14b7db868627eb788d54f720e05a8afef3c7daef MN908947/MN908947.3.txt

fdeacd60b441673fe1ecf3ab8646743e0d2cf43e5bff150c9d00b9ae6a21877e MN908947/NC_045512.2.txt

9546f6678ff97356d0d04c86e6149e866b8068211874bf47c6a65b9fc9849f75 MN938384/MN938384.txt

5f0146fb0c7251503f445af34b4f60096a6661417997fd0121e5bf2df5b8a581 MN938385.1/MN938385.1.txt

e937904b6a3942f2c6ca2db3bc728f6d25356f54b07af541de8645c39b935e85 MN938386.1/MN938386.1.txt

80fb7af766eacd1b13961b46d9f5bbfffc58e450075c9a79bb53deec5ebdf430 MN938387.1/MN938387.1.txt

c88b5f6cff88ae07738bac020b533b17d14b0a8b7144a513a51e4fdd0fe6a3c7 MN938388.1/MN938388.1.txt

b80d42374537ded079efabb8ff28717bd38b10c37befd09efca0f482a6473e4d MN938389.1/MN938389.1.txt

01d27521e01e7ea5ac42863ef7926c5ff23478c04474577ad7bf72dcd8ca4231 MN938390.1/MN938390.1.txt

96f7b2e4c1f45fda22de02a707d912dfeb8d2bef01202e539426f938096bb79b MN970003.1/MN970003.1.txt

4bb8cc4a064431dec3fcee6702658fe2220c67685f77c743ee91e5e5565d223b MN970004.1/MN970004.1.txt

861c0682e3c2a1206b55a4242c821d78d20e42b35a3401cd14a6300af72ed525 MN975262.1/MN975262.1.txt

25374d93d41f27299a46345b2faab519ed7e5f331aed66408f0643038fa1181c MN975263.1/MN975263.1.txt

cae447da935de295df1d92af26c7f45c4312e6209c15b1f07ff52620f76fc28f MN975264.1/MN975264.1.txt

0be707f3534e67aa137893d7658f33537bf091a9a75b607464619d4bd2201c9e MN975265.1/MN975265.1.txt

820ae2edc3efd512572b34f22b0823423a98e0233a8598903345f3b0dd30c243 MN975266.1/MN975266.1.txt

a2e134dc137dbc25ff446f4a8c07286acf74cfc284cbea587541bf36fc259a4b MN975267.1/MN975267.1.txt

094f862cc5514d81b1aab44833190aa06fe757ec7b29cfac4ef6bf6b0c2b0035 MN975268.1/MN975268.1.txt

b68c2f5283822cebb4a719baa89d1f63368125d96129c99f7478880528195bf9 MN985325.1/MN985325.1.txt

faedbf165c5e8461ccd95f35ac6da631103ac152ba93ecd64f74a8ee7e1a8380 MN988668.1/MN988668.1.txt

cacc0e0cd073a7b7cbc47ecdae7b13f6d1a264b9535433fc95ab0dbe8e90f4ab MN988669.1/MN988669.1.txt

2785f3b670e17189a24ddb27c391010801570ac4e67e4cc03a4b4ed0473bc42e MN988713.1/MN988713.1.txt

6d43c9c3ac4e801f3794ed3a3602d6931f6aa1941ca51b3e2440ab38d8afb588 MN994467.1/MN994467.1.txt

b2ebd83f202d52ee5c1d4ea60b635b191813386d9239290596345137cdefb566 MN994468.1/MN994468.1.txt

e01a7c295f336bd3fdffd3d0691c584eea3875a196e73f7c703304ef925e7d6f MN996527.1/MN996527.1.txt

9c2d580283048606a798de272aab817d44c44c6496e5a2a75bb200747921ab2e MN996528.1/MN996528.1.txt

505fa956d48b2706dc9a959742130f1d3273bce3256f0ad4028f97d95e59f914 MN996529.1/MN996529.1.txt

84f1bdb2b79a33f49af7b18ef84d7f9ad5bed2aac7f03d2df30bd27210dbf3e1 MN996530.1/MN996530.1.txt

4597f1df4442ebc7214db4c4e4734c79a004a51f6513515a24bc579cfdace89f MN996531.1/MN996531.1.txt

6bd51a2f882da7ce0b36db7bfdd1632c9df0ae418b008603267cf33bd89f17d3 MN997409.1/MN997409.1.txt

原文链接:https://shimo.im/docs/JJHV8HJ9VQ9PW3PQ/read

来了,老弟
-------------    本文结束  感谢您的阅读    -------------
0%