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 Bacillus subtilis strain 168 Bacillus subtilis subsp. subtilis str. 168 GCF_000009045.1_ASM904v1 SAMEA3138188 PRJNA76 2009-03-17
2 E. coli (K-12 BW25113 2014 refseq) Escherichia coli BW25113 GCF_000750555.1_ASM75055v1 SAMN03013572 PRJNA257976 2014-09-09
3 E. coli (K-12 MG1655 2013) Escherichia coli str. K-12 substr. MG1655 GCF_000005845.2_ASM584v2 SAMN02604091 PRJNA225 2013-09-26
4 Limosilactobacillus fermentum YL-11 Limosilactobacillus fermentum GCF_003860425.1_ASM386042v1 SAMN10484493 PRJNA507070 2018-12-04
5 Limosilactobacillus fermentum SRCM 103290 Limosilactobacillus fermentum GCF_004063635.1_ASM406363v1 SAMN10738354 PRJNA514937 2019-01-20
6 Limosilactobacillus fermentum AGR1487 Limosilactobacillus fermentum GCF_011032745.1_ASM1103274v1 SAMN13639333 PRJNA596816 2020-02-27
7 Limosilactobacillus fermentum AGR1485 Limosilactobacillus fermentum GCF_011032765.1_ASM1103276v1 SAMN13241836 PRJNA588334 2020-02-27
8 Mycobacterium avium (hominissuis A5 2014) Mycobacterium avium subsp. hominissuis A5 GCF_000696715.1_Maq_reference_guided_assembly SAMN02756836 PRJNA88487 2014-06-02
9 Mycobacterium palustre (DSM 44572 2017) Mycobacterium palustre GCF_002101785.1_ASM210178v1 SAMN04216940 PRJNA299467 2017-04-20
10 Mycobacterium tuberculosis (H37Rv 2013) Mycobacterium tuberculosis H37Rv GCF_000195955.2_ASM19595v2 SAMEA3138326 PRJNA224 2013-02-01
11 Plasmodium malariae (2016) Plasmodium malariae GCF_900090045.1_PmUG01 SAMEA3923181 PRJEB14392 2016-12-13
12 Pseudomonas aeruginosa (PAO1 2006) Pseudomonas aeruginosa PAO1 GCF_000006765.1_ASM676v1 SAMN02603714 PRJNA331 2006-07-07
13 Pseudomonas fluorescens (SBW25 2009) Pseudomonas fluorescens SBW25 GCF_000009225.2_ASM922v1 SAMEA2272316 PRJEA31229 2009-05-01
14 Salmonella enterica (Typhimurium LT2 2016) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 GCF_000006945.2_ASM694v2 SAMN02604315 PRJNA241 2016-01-13

Additional hubs with collections of assemblies
Collection Hub index pages: Assembly statistics: Track statistics:
Primates 57 assemblies assembly stats track stats
Mammals 348 assemblies assembly stats track stats
Birds 171 assemblies assembly stats track stats
Fishes 179 assemblies assembly stats track stats
other vertebrates 73 assemblies assembly stats track stats
Invertebrates 470 assemblies assembly stats track stats
Plants 173 assemblies assembly stats track stats
Fungi 463 assemblies assembly stats track stats
Viruses 254 assemblies assembly stats track stats
Bacteria 14 assemblies assembly stats track stats
VGP - Vertebrate Genome Project 261 assemblies assembly stats track stats
legacy/superseded 242 assemblies assembly stats track stats