8. Databases¶
8.1. EDGE provided databases¶
8.1.1. Taxnomomy Database Info Table¶
https://lanl-bioinformatics.github.io/EDGE/docs/taxonomyDBtable.html
8.1.2. NCBI Refseq¶
EDGE prebuilt blast db and bwa_index of NCBI RefSeq genomes.
- Bacteria: NCBI all complete bacteria download method
- Version: NCBI 2017 Oct 3
- 245 Archaea + 7917 Bacteria genomes
- Virus: NCBI Virus
- Version: NCBI 2017 Oct 3
- 7458 complete genomes + Neighbor Nucleotoides (118039 seuqences)
see $EDGE_HOME/database/bwa_index/id_mapping.txt for all gi/accession to genome name lookup table.
8.1.3. Krona taxonomy¶
- paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=21961884
- website: http://sourceforge.net/p/krona/home/krona/
8.1.3.1. Update Krona taxonomy db¶
Go to the folder in the KronaTools installation and run (internet required)
cd $EDGE_HOME/thirdParty/KronaTools-2.7/
./updateTaxonomy.sh
./updateAccessions.sh
This uses about 16 GB of disk space and an additional 16 GB of scratch space during installation (at the time of this writing; it is always growing) and takes minutes or up to an hour to run.
8.1.4. Metaphlan4 database¶
MetaPhlAn 4 relies on ~5.1M unique clade-specific marker genes identified from ~1M microbial genomes (~236,600 references and 771,500 metagenomic assembled genomes) spanning 26,970 species-level genome bins (SGBs, http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html), 4,992 of them taxonomically unidentified at the species level.
8.1.5. Human Genome¶
The bwa index is prebuilt in the EDGE. The human hs_ref_GRCh38 sequences from NCBI ftp site.
8.1.6. Kraken2 DB¶
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Kraken2 database in EDGE is a pre-built database constructed from Refseq bacteria, archaea, and viral libraries and the GRCh38 human genome and UniVec_Core in RefSeq (as of Dec, 2021).
- Kraken1 paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=24580807
- website: http://ccb.jhu.edu/software/kraken2/
8.1.7. Centrifuge DB¶
Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The database includes human genome, prokaryotic genomes, and viral genomes including 106 SARS-CoV-2 complete genomes. (as of Mar 29, 2020)
- Centrifuge paper: https://pubmed.ncbi.nlm.nih.gov/27852649/
- website: https://ccb.jhu.edu/software/centrifuge/
8.1.8. GOTTCHA DB¶
A novel, annotation-independent and signature-based metagenomic taxonomic profiling tool.
- website: http://lanl-bioinformatics.github.io/GOTTCHA/
- ftp: https://edge-dl.lanl.gov/gottcha/
- version: v20150825
8.1.9. SNPdb¶
SNP database based on whole genome comparison. Current available db are Ecoli, Yersinia, Francisella, Brucella, Bacillus .
8.1.10. Invertebrate Vectors of Human Pathogens¶
The bwa index is prebuilt in the EDGE.
version: 2014 July 24
8.1.11. NCBI Nucleotide database (NT) database¶
- website: ftp://ftp.ncbi.nih.gov/blast/db/
- version: 2016 April 26
8.1.12. VFDB¶
A Microbial database of virulence factors
- paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=26578559
- website: http://www.mgc.ac.cn/VFs/main.htm
- version: 20160818
8.1.13. ARDB¶
Antibiotic Resistance Genes Database
- website: http://ardb.cbcb.umd.edu/index.html
- version: 1.1
8.1.14. CARD¶
The Comprehensive Antibiotic Resistance Database
- website: https://card.mcmaster.ca/
- Version: 3.0.7
8.1.15. Amplicon: 16s/18s/ITS¶
For QIIME (Quantitative insights into Microbial Ecology) analysis (scikit-learn=0.24.1)
- Greengenes OTUs (16s)
- website: http://greengenes.secondgenome.com/
- version: 2022_10
- SILVA OTUs (16S/18S)
- website: http://www.arb-silva.de/download/archive/qiime/
- version: 138
- UNITE OTUs (Fungal ITS)
- website: https://unite.ut.ee/repository.php
- version: 16.10.2022
8.2. Building bwa index¶
Here take human genome as example.
Download the human hs_ref_GRCh38 sequences from NCBI ftp site:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_genomic.fna.gz
Use the installed bwa to build the index:
$EDGE_HOME/bin/bwa index -p human_ref_GRCh38 GCA_000001405.28_GRCh38.p13_genomic.fna.gz
Now, you can configure the config file with “host=/path/to/human_ref_GRCh38” for host removal step.
8.3. SNP database genomes¶
SNP database was pre-built from the below genomes.
8.3.1. Ecoli Genomes¶
| Name | Description | URL |
|---|---|---|
| Ecoli_042 | Escherichia coli 042, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387605479 |
| Ecoli_11128 | Escherichia coli O111:H- str. 11128, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/260866153 |
| Ecoli_11368 | Escherichia coli O26:H11 str. 11368 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/260853213 |
| Ecoli_12009 | Escherichia coli O103:H2 str. 12009, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/260842239 |
| Ecoli_2009EL2050 | Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/410480139 |
| Ecoli_2009EL2071 | Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/407466711 |
| Ecoli_2011C3493 | Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/407479587 |
| Ecoli_536 | Escherichia coli 536, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/110640213 |
| Ecoli_55989 | Escherichia coli 55989 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218693476 |
| Ecoli_ABU_83972 | Escherichia coli ABU 83972 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386637352 |
| Ecoli_APEC_O1 | Escherichia coli APEC O1 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/117622295 |
| Ecoli_ATCC_8739 | Escherichia coli ATCC 8739 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/170018061 |
| Ecoli_BL21_DE3 | Escherichia coli BL21(DE3) chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387825439 |
| Ecoli_BW2952 | Escherichia coli BW2952 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/238899406 |
| Ecoli_CB9615 | Escherichia coli O55:H7 str. CB9615 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/291280824 |
| Ecoli_CE10 | Escherichia coli O7:K1 str. CE10 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386622414 |
| Ecoli_CFT073 | Escherichia coli CFT073 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/26245917 |
| Ecoli_DH1 | Escherichia coli DH1, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387619774 |
| Ecoli_Di14 | Escherichia coli str. ‘clone D i14’ chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386632422 |
| Ecoli_Di2 | Escherichia coli str. ‘clone D i2’ chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386627502 |
| Ecoli_E2348_69 | Escherichia coli O127:H6 str. E2348/69 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/215485161 |
| Ecoli_E24377A | Escherichia coli E24377A chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/157154711 |
| Ecoli_EC4115 | Escherichia coli O157:H7 str. EC4115 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/209395693 |
| Ecoli_ED1a | Escherichia coli ED1a chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218687878 |
| Ecoli_EDL933 | Escherichia coli O157:H7 str. EDL933 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/16445223 |
| Ecoli_ETEC_H10407 | Escherichia coli ETEC H10407, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387610477 |
| Ecoli_HS | Escherichia coli HS, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/157159467 |
| Ecoli_IAI1 | Escherichia coli IAI1 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218552585 |
| Ecoli_IAI39 | Escherichia coli IAI39 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218698419 |
| Ecoli_IHE3034 | Escherichia coli IHE3034 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386597751 |
| Ecoli_K12_DH10B | Escherichia coli str. K-12 substr. DH10B chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/170079663 |
| Ecoli_K12_MG1655 | Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/49175990 |
| Ecoli_K12_W3110 | Escherichia coli str. K-12 substr. W3110, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/388476123 |
| Ecoli_KO11FL | Escherichia coli KO11FL chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386698504 |
| Ecoli_LF82 | Escherichia coli LF82, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/222154829 |
| Ecoli_NA114 | Escherichia coli NA114 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386617516 |
| Ecoli_NRG_857C | Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387615344 |
| Ecoli_P12b | Escherichia coli P12b chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386703215 |
| Ecoli_REL606 | Escherichia coli B str. REL606 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/254160123 |
| Ecoli_RM12579 | Escherichia coli O55:H7 str. RM12579 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387504934 |
| Ecoli_S88 | Escherichia coli S88 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218556939 |
| Ecoli_SE11 | Escherichia coli O157:H7 str. Sakai chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/15829254 |
| Ecoli_SE15 | Escherichia coli SE11 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/209917191 |
| Ecoli_SMS35 | Escherichia coli SE15, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387828053 |
| Ecoli_Sakai | Escherichia coli SMS-3-5 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/170679574 |
| Ecoli_TW14359 | Escherichia coli O157:H7 str. TW14359 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/254791136 |
| Ecoli_UM146 | Escherichia coli UM146 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386602643 |
| Ecoli_UMN026 | Escherichia coli UMN026 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218703261 |
| Ecoli_UMNK88 | Escherichia coli UMNK88 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386612163 |
| Ecoli_UTI89 | Escherichia coli UTI89 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/91209055 |
| Ecoli_W | Escherichia coli W chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386707734 |
| Ecoli_Xuzhou21 | Escherichia coli Xuzhou21 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/387880559 |
| Sboydii_CDC_3083_94 | Shigella boydii CDC 3083-94 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/187730020 |
| Sboydii_Sb227 | Shigella boydii Sb227 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/82542618 |
| Sdysenteriae_Sd197 | Shigella dysenteriae Sd197, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/82775382 |
| Sflexneri_2002017 | Shigella flexneri 2002017 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384541581 |
| Sflexneri_2a_2457T | Shigella flexneri 2a str. 2457T, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/30061571 |
| Sflexneri_2a_301 | Shigella flexneri 2a str. 301 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/344915202 |
| Sflexneri_5_8401 | Shigella flexneri 5 str. 8401 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/110804074 |
| Ssonnei_53G | Shigella sonnei 53G, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/377520096 |
| Ssonnei_Ss046 | Shigella sonnei Ss046 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/74310614 |
8.3.2. Yersinia Genomes¶
| Name | Description | URL |
|---|---|---|
| Ypestis_A1122 | Yersinia pestis A1122 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384137007 |
| Ypestis_Angola | Yersinia pestis Angola chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/162418099 |
| Ypestis_Antiqua | Yersinia pestis Antiqua chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/108805998 |
| Ypestis_CO92 | Yersinia pestis CO92 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/16120353 |
| Ypestis_D106004 | Yersinia pestis D106004 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384120592 |
| Ypestis_D182038 | Yersinia pestis D182038 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384124469 |
| Ypestis_KIM_10 | Yersinia pestis KIM 10 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/22123922 |
| Ypestis_Medievalis_Harbin_35 | Yersinia pestis biovar Medievalis str. Harbin 35 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384412706 |
| Ypestis_Microtus_91001 | Yersinia pestis biovar Microtus str. 91001 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/45439865 |
| Ypestis_Nepal516 | Yersinia pestis Nepal516 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/108810166 |
| Ypestis_Pestoides_F | Yersinia pestis Pestoides F chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/145597324 |
| Ypestis_Z176003 | Yersinia pestis Z176003 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/294502110 |
| Ypseudotuberculosis_IP_31758 | Yersinia pseudotuberculosis IP 31758 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/153946813 |
| Ypseudotuberculosis_IP_32953 | Yersinia pseudotuberculosis IP 32953 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/51594359 |
| Ypseudotuberculosis_PB1 | Yersinia pseudotuberculosis PB1/+ chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/186893344 |
| Ypseudotuberculosis_YPIII | Yersinia pseudotuberculosis YPIII chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/170022262 |
8.3.3. Francisella Genomes¶
| Name | Description | URL |
|---|---|---|
| Fnovicida_U112 | Francisella novicida U112 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/118496615 |
| Ftularensis_holarctica_F92 | Francisella tularensis subsp. holarctica F92 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/423049750 |
| Ftularensis_holarctica_FSC200 | Francisella tularensis subsp. holarctica FSC200 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/422937995 |
| Ftularensis_holarctica_FTNF00200 | Francisella tularensis subsp. holarctica FTNF002-00 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/156501369 |
| Ftularensis_holarctica_LVS | Francisella tularensis subsp. holarctica LVS chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/89255449 |
| Ftularensis_holarctica_OSU18 | Francisella tularensis subsp. holarctica OSU18 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/115313981 |
| Ftularensis_mediasiatica_FSC147 | Francisella tularensis subsp. mediasiatica FSC147 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/187930913 |
| Ftularensis_TIGB03 | Francisella tularensis TIGB03 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/379716390 |
| Ftularensis_tularensis_FSC198 | Francisella tularensis subsp. tularensis FSC198 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/110669657 |
| Ftularensis_tularensis_NE061598 | Francisella tularensis subsp. tularensis NE061598 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/385793751 |
| Ftularensis_tularensis_SCHU_S4 | Francisella tularensis subsp. tularensis SCHU S4 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/255961454 |
| Ftularensis_tularensis_TI0902 | Francisella tularensis subsp. tularensis TI0902 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/379725073 |
| Ftularensis_tularensis_WY963418 | Francisella tularensis subsp. tularensis WY96-3418 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/134301169 |
8.3.4. Brucella Genomes¶
| Name | Description | URL |
|---|---|---|
| Babortus_1_9941 | Brucella abortus bv. 1 str. 9-941 | http://www.ncbi.nlm.nih.gov/bioproject/58019 |
| Babortus_A13334 | Brucella abortus A13334 | http://www.ncbi.nlm.nih.gov/bioproject/83615 |
| Babortus_S19 | Brucella abortus S19 | http://www.ncbi.nlm.nih.gov/bioproject/58873 |
| Bcanis_ATCC_23365 | Brucella canis ATCC 23365 | http://www.ncbi.nlm.nih.gov/bioproject/59009 |
| Bcanis_HSK_A52141 | Brucella canis HSK A52141 | http://www.ncbi.nlm.nih.gov/bioproject/83613 |
| Bceti_TE10759_12 | Brucella ceti TE10759-12 | http://www.ncbi.nlm.nih.gov/bioproject/229880 |
| Bceti_TE28753_12 | Brucella ceti TE28753-12 | http://www.ncbi.nlm.nih.gov/bioproject/229879 |
| Bmelitensis_1_16M | Brucella melitensis bv. 1 str. 16M | http://www.ncbi.nlm.nih.gov/bioproject/200008 |
| Bmelitensis_Abortus_2308 | Brucella melitensis biovar Abortus 2308 | http://www.ncbi.nlm.nih.gov/bioproject/16203 |
| Bmelitensis_ATCC_23457 | Brucella melitensis ATCC 23457 | http://www.ncbi.nlm.nih.gov/bioproject/59241 |
| Bmelitensis_M28 | Brucella melitensis M28 | http://www.ncbi.nlm.nih.gov/bioproject/158857 |
| Bmelitensis_M590 | Brucella melitensis M5-90 | http://www.ncbi.nlm.nih.gov/bioproject/158855 |
| Bmelitensis_NI | Brucella melitensis NI | http://www.ncbi.nlm.nih.gov/bioproject/158853 |
| Bmicroti_CCM_4915 | Brucella microti CCM 4915 | http://www.ncbi.nlm.nih.gov/bioproject/59319 |
| Bovis_ATCC_25840 | Brucella ovis ATCC 25840 | http://www.ncbi.nlm.nih.gov/bioproject/58113 |
| Bpinnipedialis_B2_94 | Brucella pinnipedialis B2/94 | http://www.ncbi.nlm.nih.gov/bioproject/71133 |
| Bsuis_1330 | Brucella suis 1330 | http://www.ncbi.nlm.nih.gov/bioproject/159871 |
| Bsuis_ATCC_23445 | Brucella suis ATCC 23445 | http://www.ncbi.nlm.nih.gov/bioproject/59015 |
| Bsuis_VBI22 | Brucella suis VBI22 | http://www.ncbi.nlm.nih.gov/bioproject/83617 |
8.3.5. Bacillus Genomes¶
| Name | Description | URL |
|---|---|---|
| Banthracis_A0248 | Bacillus anthracis str. A0248, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/229599883 |
| Banthracis_Ames | Bacillus anthracis str. ‘Ames Ancestor’ chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/50196905 |
| Banthracis_Ames_Ancestor | Bacillus anthracis str. Ames chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/30260195 |
| Banthracis_CDC_684 | Bacillus anthracis str. CDC 684 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/227812678 |
| Banthracis_H9401 | Bacillus anthracis str. H9401 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/386733873 |
| Banthracis_Sterne | Bacillus anthracis str. Sterne chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/49183039 |
| Bcereus_03BB102 | Bacillus cereus 03BB102, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/225862057 |
| Bcereus_AH187 | Bacillus cereus AH187 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/217957581 |
| Bcereus_AH820 | Bacillus cereus AH820 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218901206 |
| Bcereus_anthracis_CI | Bacillus cereus biovar anthracis str. CI chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/301051741 |
| Bcereus_ATCC_10987 | Bacillus cereus ATCC 10987 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/42779081 |
| Bcereus_ATCC_14579 | Bacillus cereus ATCC 14579, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/30018278 |
| Bcereus_B4264 | Bacillus cereus B4264 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218230750 |
| Bcereus_E33L | Bacillus cereus E33L chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/52140164 |
| Bcereus_F837_76 | Bacillus cereus F837/76 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/376264031 |
| Bcereus_G9842 | Bacillus cereus G9842 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/218895141 |
| Bcereus_NC7401 | Bacillus cereus NC7401, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/375282101 |
| Bcereus_Q1 | Bacillus cereus Q1 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/222093774 |
| Bthuringiensis_AlHakam | Bacillus thuringiensis str. Al Hakam chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/118475778 |
| Bthuringiensis_BMB171 | Bacillus thuringiensis BMB171 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/296500838 |
| Bthuringiensis_Bt407 | Bacillus thuringiensis Bt407 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/409187965 |
| Bthuringiensis_chinensis_CT43 | Bacillus thuringiensis serovar chinensis CT-43 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384184088 |
| Bthuringiensis_finitimus_YBT020 | Bacillus thuringiensis serovar finitimus YBT-020 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/384177910 |
| Bthuringiensis_konkukian_9727 | Bacillus thuringiensis serovar konkukian str. 97-27 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/49476684 |
| Bthuringiensis_MC28 | Bacillus thuringiensis MC28 chromosome, complete genome | http://www.ncbi.nlm.nih.gov/nuccore/407703236 |
8.4. Ebola Reference Genomes¶
| Accession | Description | URL |
|---|---|---|
| NC_014372 | Tai Forest ebolavirus isolate Tai Forest virus H.sapiens-tc/CIV/1994/Pauleoula-CI, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/NC_014372 |
| FJ217162 | Cote d’Ivoire ebolavirus, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/FJ217162 |
| FJ968794 | Sudan ebolavirus strain Boniface, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/FJ968794 |
| NC_006432 | Sudan ebolavirus isolate Sudan virus H.sapiens-tc/UGA/2000/Gulu-808892, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/NC_006432 |
| KJ660348 | Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C05, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KJ660348 |
| KJ660347 | Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Gueckedou-C07, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KJ660347 |
| KJ660346 | Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Kissidougou-C15, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KJ660346 |
| JN638998 | Sudan ebolavirus - Nakisamata, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/JN638998 |
| AY354458 | Zaire ebolavirus strain Zaire 1995, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/AY354458 |
| AY729654 | Sudan ebolavirus strain Gulu, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/AY729654 |
| EU338380 | Sudan ebolavirus isolate EBOV-S-2004 from Sudan, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/EU338380 |
| KM655246 | Zaire ebolavirus isolate H.sapiens-tc/COD/1976/Yambuku-Ecran, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KM655246 |
| KC242801 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1976/deRoover, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242801 |
| KC242800 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/2002/Ilembe, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242800 |
| KC242799 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1995/13709 Kikwit, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242799 |
| KC242798 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Ikot, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242798 |
| KC242797 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Oba, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242797 |
| KC242796 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1995/13625 Kikwit, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242796 |
| KC242795 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Mbie, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242795 |
| KC242794 | Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/2Nza, complete genome. | http://www.ncbi.nlm.nih.gov/nuccore/KC242794 |