Bacteria Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, subset of bacteria only.

How to view the hub

Options:

  1. The links to the genome browser in the table below will attach that one specific assembly to the genome browser. This is most likely what you want. Alternatively, the entire set of assemblies can be attached as one group to the genome browser with the following links depending upon which of our mirror site browsers you prefer to use:
    attach all assemblies to selected site:   genome.ucsc.edu   genome-euro.ucsc.edu   genome-asia.ucsc.edu
  2. To manually attach all the assemblies in this hub to genome browsers that are not one of the three UCSC mirror sites:
    1. From the blue navigation bar, go to My Data -> Track Hubs
    2. Then select the My Hubs tab and enter this URL into the textbox:
      https://hgdownload.soe.ucsc.edu/hubs/bacteria/hub.txt
    3. Once you have added the URL to the entry form, press the Add Hub button to add the hub.

After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the Bacteria Hub Assembly dropdown menu. Instead of adding all the assemblies in one collected group, use the individual view in browser in the table below.

See also: assembly statistics, track statistics <== additional information for these assemblies.


Data resource links

NOTE: Click on the column headers to sort the table by that column

The common name and view in browser will attach only that single assembly to the genome browser.
The scientific name and data download link provides access to the files for that one assembly hub.
The other links provide access to NCBI resources for these assemblies.
count common name and
view in browser		 scientific name
and data download		 NCBI assembly BioSample BioProject assembly date,
source link
1 Acinetobacter baumannii (17978UN 2021) Acinetobacter baumannii GCF_019356215.1_ASM1935621v1 SAMN20326334 PRJNA748365 2021-07-27
2 Acinetobacter baumannii (ATCC 17978 2021) Acinetobacter baumannii ATCC 17978 GCA_902728005.1_Acinetobacter_baumannii_ATCC17978 SAMEA6463085 PRJEB36129 2021-03-25
3 Acinetobacter baumannii (ATCC 19606 2016) Acinetobacter baumannii GCA_900011295.1_ATCC19606_assembly SAMEA3650403 PRJEB10709 2016-04-11
4 Actinobacillus pleuropneumoniae serovar 5b (L20 2007) Actinobacillus pleuropneumoniae serovar 5b str. L20 GCA_000015885.1_ASM1588v1 SAMN02603665 PRJNA18221 2007-02-23
5 Anaplasma phagocytophilum str. (HGE1 2013) Anaplasma phagocytophilum str. HGE1 GCA_000478425.1_ASM47842v1 SAMN02471893 PRJNA171710 2013-04-23
6 Arthrobacter sp. SLBN-53 (NRRL B-3805 2016) Arthrobacter sp. SLBN-53 GCA_001580405.1_ASM158040v1 SAMN03396774 PRJNA266535 2016-03-07
7 Bacillus mojavensis (PS17 2020) Bacillus mojavensis GCA_016413745.1_ASM1641374v1 SAMN17051132 PRJNA684065 2020-12-28
8 Bacillus subtilis strain 168 Bacillus subtilis subsp. subtilis str. 168 GCF_000009045.1_ASM904v1 SAMEA3138188 PRJNA76 2009-03-17
9 Bacillus subtilis (NCD-2 2017) Bacillus subtilis subsp. subtilis GCA_002556525.1_ASM255652v1 SAMN07672787 PRJNA408006 2017-10-16
10 Burkholderia multivorans (ATCC 17616 2007) Burkholderia multivorans ATCC 17616 GCA_000018505.1_ASM1850v1 SAMN00623032 PRJNA17407 2007-11-15
11 Clostridium butyricum (DSM 10702 2020) Clostridium butyricum GCA_014131795.1_ASM1413179v1 SAMN11835364 PRJNA544389 2020-08-10
12 Corynebacterium glutamicum (ATCC 13032 2004) Corynebacterium glutamicum ATCC 13032 GCA_000011325.1_ASM1132v1 SAMD00061105 PRJNA307 2004-02-18
13 Desulfovibrio desulfuricans (DSM 642 2013) Desulfovibrio desulfuricans DSM 642 GCA_000420465.1_ASM42046v1 SAMN02440572 PRJNA185532 2013-07-09
14 Desulfovibrio vulgaris str. (Hildenborough 2004) Desulfovibrio vulgaris str. Hildenborough GCA_000195755.1_ASM19575v1 SAMN02603973 PRJNA51 2004-04-21
15 E. coli (B C2566 2016) Escherichia coli B GCF_001559615.2_ASM155961v2 SAMN04435507 PRJNA309539 2016-06-15
16 E. coli (B C3029 2016) Escherichia coli B GCF_001559635.1_ASM155963v1 SAMN04435508 PRJNA309540 2016-02-11
17 E. coli (BE104 2019) Escherichia coli GCF_005890115.1_ASM589011v1 SAMN11841626 PRJNA544505 2019-05-30
18 E. coli (BL21(DE3) 2010) Escherichia coli BL21(DE3) GCA_000022665.2_ASM2266v1 SAMN02603478 PRJNA20713 2010-05-17
19 E. coli (K-12 BW25113 2014 refseq) Escherichia coli BW25113 GCF_000750555.1_ASM75055v1 SAMN03013572 PRJNA257976 2014-09-09
20 E. coli (K-12 C3026 2016) Escherichia coli K-12 GCF_001559675.1_ASM155967v1 SAMN04435499 PRJNA309537 2016-02-11
21 E. coli (K-12 DHB4 2016) Escherichia coli K-12 GCF_001559655.1_ASM155965v1 SAMN04435497 PRJNA309536 2016-02-11
22 E. coli (K-12 MG1655 2013) Escherichia coli str. K-12 substr. MG1655 GCF_000005845.2_ASM584v2 SAMN02604091 PRJNA225 2013-09-26
23 E. coli (Nissle 1917 2014) Escherichia coli Nissle 1917 GCA_000714595.1_ASM71459v1 SAMN02794012 PRJNA248167 2014-06-27
24 Janthinobacterium (BJB312 2017) Janthinobacterium sp. BJB312 GCA_002735715.1_ASM273571v1 SAMN03098205 PRJNA251750 2017-10-28
25 Janthinobacterium (BJB1 2017) Janthinobacterium sp. BJB1 GCA_002735775.2_ASM273577v2 SAMN02839584 PRJNA251750 2017-11-16
26 Klebsiella aerogenes (KCTC 2190 2011) Klebsiella aerogenes KCTC 2190 GCA_000215745.1_ASM21574v1 SAMN02603581 PRJNA66537 2011-06-03
27 Klebsiella pneumoniae (ATCC BAA-2146 2016) Klebsiella pneumoniae GCA_000364385.3_ASM36438v3 SAMN02152539 PRJNA183901 2016-01-04
28 Lacticaseibacillus paracasei (LC2W 2011) Lacticaseibacillus paracasei GCA_000194785.1_ASM19478v1 SAMN02603877 PRJNA64433 2011-04-01
29 Lactobacillus kefiranofaciens (KR 2017) Lactobacillus kefiranofaciens GCA_002276565.1_ASM227656v1 SAMN06718494 PRJNA375758 2017-08-29
30 Lactobacillus kefiranofaciens (ATCC 43761 2016) Lactobacillus kefiranofaciens GCA_900103655.1_IMG-taxon_2597490363_annotated_assembly SAMN02983011 PRJEB16188 2016-10-21
31 Lactobacillus kefiranofaciens (JCM 6985 DSM 5016 2014) Lactobacillus kefiranofaciens subsp. kefiranofaciens DSM 5016 = JCM 6985 GCA_000615685.1_ASM61568v1 SAMD00008926 PRJDB645 2014-03-31
32 Lactobacillus kefiranofaciens (JCM 6985 DSM 5016 2015) Lactobacillus kefiranofaciens subsp. kefiranofaciens DSM 5016 = JCM 6985 GCA_001435275.1_ASM143527v1 SAMN02369453 PRJNA222257 2015-11-06
33 Lactobacillus kefiranofaciens (ASM143419v1 JCM 8572 DSM 10550 2015) Lactobacillus kefiranofaciens subsp. kefirgranum DSM 10550 = JCM 8572 GCA_001434195.1_ASM143419v1 SAMN02369454 PRJNA222257 2015-11-06
34 Lactobacillus kefiranofaciens (ASM131133v1 JCM 8572 JSM 10550 2015) Lactobacillus kefiranofaciens subsp. kefirgranum DSM 10550 = JCM 8572 GCA_001311335.1_ASM131133v1 SAMD00000473 PRJDB772 2015-10-01
35 Lactobacillus kefiranofaciens (LKK75 2019) Lactobacillus kefiranofaciens subsp. kefiranofaciens GCA_009184665.1_ASM918466v1 SAMN12792932 PRJNA566025 2019-10-20
36 Lactobacillus kefiranofaciens (ZW3 2011) Lactobacillus kefiranofaciens subsp. kefiranofaciens GCA_000214785.1_ASM21478v1 SAMN02603965 PRJNA66525 2011-05-25
37 Lactococcus lactis (IL1403 2018) Lactococcus lactis GCA_003722275.1_ASM372227v1 SAMN10387363 PRJNA503975 2018-11-13
38 Leuconostoc citreum (KM20 2008) Leuconostoc citreum KM20 GCA_000026405.1_ASM2640v1 SAMN02603482 PRJNA16062 2008-03-12
39 Limosilactobacillus fermentum AGR1485 Limosilactobacillus fermentum GCF_011032765.1_ASM1103276v1 SAMN13241836 PRJNA588334 2020-02-27
40 Limosilactobacillus fermentum AGR1487 Limosilactobacillus fermentum GCF_011032745.1_ASM1103274v1 SAMN13639333 PRJNA596816 2020-02-27
41 Limosilactobacillus fermentum SRCM 103290 Limosilactobacillus fermentum GCF_004063635.1_ASM406363v1 SAMN10738354 PRJNA514937 2019-01-20
42 Limosilactobacillus fermentum YL-11 Limosilactobacillus fermentum GCF_003860425.1_ASM386042v1 SAMN10484493 PRJNA507070 2018-12-04
43 Lysinibacillus sphaericus (C3-41 2008) Lysinibacillus sphaericus C3-41 GCA_000017965.1_ASM1796v1 SAMN02604328 PRJNA19619 2008-02-27
44 Methylorubrum extorquens (CM4 2008) Methylorubrum extorquens CM4 GCA_000021845.1_ASM2184v1 SAMN00000037 PRJNA19527 2008-12-19
45 Mycobacterium avium (hominissuis A5 2014) Mycobacterium avium subsp. hominissuis A5 GCF_000696715.1_Maq_reference_guided_assembly SAMN02756836 PRJNA88487 2014-06-02
46 Mycobacterium palustre (DSM 44572 2017) Mycobacterium palustre GCF_002101785.1_ASM210178v1 SAMN04216940 PRJNA299467 2017-04-20
47 Mycobacterium sp. (VKM Ac-1817D 2014) Mycobacterium sp. VKM Ac-1817D GCA_000416365.2_ASM41636v2 SAMN02469803 PRJNA183985 2014-11-25
48 Mycobacterium tuberculosis (ASM19595v2 H37Rv 2013) Mycobacterium tuberculosis H37Rv GCF_000195955.2_ASM19595v2 SAMEA3138326 PRJNA224 2013-02-01
49 Mycobacterium tuberculosis (ASM27773v2 H37Rv 2013) Mycobacterium tuberculosis H37Rv GCA_000277735.2_ASM27773v2 SAMN03081436 PRJNA37301 2013-11-26
50 Neisseria meningitidis (Z2491 2003) Neisseria meningitidis Z2491 GCA_000009105.1_ASM910v1 SAMEA1705949 PRJNA252 2003-05-06
51 Nitratireductor (SY7 2020) Nitratireductor sp. SY7 GCA_007922615.2_ASM792261v2 SAMN12400551 PRJNA557672 2020-04-03
52 Nitrosomonas europaea (ATCC 19718 2003) Nitrosomonas europaea ATCC 19718 GCA_000009145.1_ASM914v1 SAMEA3138193 PRJNA52 2003-05-06
53 Pectobacterium brasiliense (1692 2020) Pectobacterium brasiliense GCA_009873295.1_ASM987329v1 SAMN13779957 PRJNA599934 2020-01-14
54 Plasmodium malariae (2016) Plasmodium malariae GCF_900090045.1_PmUG01 SAMEA3923181 PRJEB14392 2016-12-13
55 Pseudomonas aeruginosa (PAO1 2006) Pseudomonas aeruginosa PAO1 GCF_000006765.1_ASM676v1 SAMN02603714 PRJNA331 2006-07-07
56 Pseudomonas fluorescens (SBW25 2009) Pseudomonas fluorescens SBW25 GCF_000009225.2_ASM922v1 SAMEA2272316 PRJEA31229 2009-05-01
57 Rhodococcus erythropolis (CCM2595 2013) Rhodococcus erythropolis CCM2595 GCA_000454045.1_ASM45404v1 SAMN02603403 PRJNA81583 2013-08-22
58 Salmonella enterica (Typhimurium LT2 2016) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 GCF_000006945.2_ASM694v2 SAMN02604315 PRJNA241 2016-01-13
59 Salmonella enterica subsp. enterica serovar Typhimurium str. (14028S 2009) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S GCA_000022165.1_ASM2216v1 SAMN02604137 PRJNA33067 2009-11-13
60 Shigella flexneri 5a (M90T 2019) Shigella flexneri 5a str. M90T GCA_004799585.1_ASM479958v1 SAMN10608416 PRJNA510559 2019-04-18
61 Staphylococcus aureus (JE2 2017) Staphylococcus aureus GCA_002085525.1_ASM208552v1 SAMN06677988 PRJNA381486 2017-04-11
62 Starmerella bacillaris (NP2 2017) Starmerella bacillaris GCA_002270425.1_ASM227042v1 SAMN07482632 PRJNA397468 2017-08-25
63 Streptomyces bottropensis (ATCC 25435 2013) Streptomyces bottropensis ATCC 25435 GCA_000383595.1_ASM38359v1 SAMN02261243 PRJNA104983 2013-04-26
64 Stutzerimonas degradans (XL272 2019) Stutzerimonas degradans GCA_009740185.1_ASM974018v1 SAMN13482974 PRJNA593625 2019-12-11

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 58 assemblies assembly stats track stats
Mammals 377 assemblies assembly stats track stats
Birds 235 assemblies assembly stats track stats
Fishes 246 assemblies assembly stats track stats
other vertebrates 82 assemblies assembly stats track stats
Invertebrates 509 assemblies assembly stats track stats
Plants 207 assemblies assembly stats track stats
Fungi 537 assemblies assembly stats track stats
Viruses 256 assemblies assembly stats track stats
Bacteria 64 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 435 assemblies assembly stats track stats
legacy/superseded 300 assemblies assembly stats track stats