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.

paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=36823356
website: http://huttenhower.sph.harvard.edu/metaphlan4

8.1.5. Human Genome

The bwa index is prebuilt in the EDGE. The human hs_ref_GRCh38 sequences from NCBI ftp site.

website https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38/

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.

paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=22135296
website: https://www.vectorbase.org

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