8. Databases¶
8.1. EDGE provided databases¶
8.1.1. MvirDB¶
A Microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defense applications
8.1.2. NCBI Refseq¶
EDGE prebuilt blast db and bwa_index of NCBI RefSeq genomes.
- Bacteria: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/all.fna.tar.gz
- Version: NCBI 2015 Aug 11
- 2786 genomes
- Virus: NCBI Virus
- Version: NCBI 2015 Aug 11
- 4834 RefSeq + Neighbor Nucleotoides (51300 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¶
Download these files from ftp://ftp.ncbi.nih.gov/pub/taxonomy:
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz
wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
Transfer the files to the taxonomy folder in the standalone KronaTools installation and run:
$EDGE_HOME/thirdParty/KronaTools-2.4/updateTaxonomy.sh --local.
8.1.4. Metaphlan database¶
MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes.
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. MiniKraken DB¶
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. MiniKraken is a pre-built 4 GB database constructed from complete bacterial, archaeal, and viral genomes in RefSeq (as of Mar. 30, 2014).
8.1.7. GOTTCHA DB¶
A novel, annotation-independent and signature-based metagenomic taxonomic profiling tool. (manuscript in submission)
8.1.8. SNPdb¶
SNP database based on whole genome comparison. Current available db are Ecoli, Yersinia, Francisella, Brucella, Bacillus .
8.1.9. Invertebrate Vectors of Human Pathogens¶
The bwa index is prebuilt in the EDGE.
Version: 2014 July 24
8.1.10. Other optional database¶
Not in the EDGE but you can download.
- NCBI nr/nt blastDB: ftp://ftp.ncbi.nih.gov/blast/db/
8.2. Building bwa index¶
Here take human genome as example.
- Download the human hs_ref_GRCh38 sequences from NCBI ftp site.
Go to ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/seq/ Or use a provided perl script in $EDGE_HOME/scripts/
perl $EDGE_HOME/scripts/download_human_refseq_genome.pl output_dir
Gunzip the downloaded fasta file and concatenate them into one human genome multifasta file:
gunzip hs_ref_GRCh38.*.fa.gz cat hs_ref_GRCh38.*.fa > human_ref_GRCh38.all.fasta
Use the installed bwa to build the index:
$EDGE_HOME/bin/bwa index human_ref_GRCh38.all.fasta
Now, you can configure the config file with “host=/path/human_ref_GRCh38.all.fasta” 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 |