This repository provides sequence data for our phylogenomic study of E. coli ST131 in an easily accessible format. If you use this data in your publications please cite:
PETTY NK*, BEN ZAKOUR NL*, STANTON-COOK M, SKIPPINGTON E, TOTSIKA M, FORDE BM, PHAN MD, MORIEL D, PETERS KM, DAVIES MR, ROGERS BA, DOUGAN G, RODRIGUEZ-BAÑO J, PASCUAL A, PITOUT JDD, UPTON M, PATERSON DL, WALSH TR, SCHEMBRI MA^, BEATSON SA^. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci USA (in press). ^CORRESPONDING AUTHORS *AUTHORS CONTRIBUTED EQUALLY
The Illumina sequencing reads are available under the ENA accessions PRJEB2968 (95 paired reads) and PRJEB5004 (4 paired reads).
The following table facilitates this:
| Strain | Accession |
|---|---|
| HVM2757 | ERR161327 |
| HVM1181 | ERR161319 |
| P112EC | ERR161312 |
| HVM2049 | ERR161324 |
| S2EC | ERR161235 |
| S26EC | ERR161245 |
| S37EC | ERR161302 |
| S31EC | ERR161300 |
| S5EC | ERR161236 |
| S94EC | ERR161257 |
| S120EC | ERR161283 |
| S34EC | ERR161247 |
| S79EC | ERR161305 |
| S128EC | ERR161291 |
| S104EC | ERR161267 |
| S105EC | ERR161268 |
| S21EC | ERR161242 |
| S22EC | ERR161243 |
| HVM1147 | ERR161318 |
| S24EC | ERR161244 |
| S6EC | ERR161299 |
| S114EC | ERR161277 |
| S32EC | ERR161301 |
| S19EC | ERR161241 |
| HVM277 | ERR161315 |
| HVM52 | ERR161308 |
| HVM2044 | ERR161323 |
| HVM2289 | ERR161325 |
| S77EC | ERR161304 |
| S115EC | ERR161278 |
| S103EC | ERR161266 |
| S65EC | ERR161303 |
| IR18E | ERR458470 |
| S119EC | ERR161282 |
| S118EC | ERR161281 |
| HVM1299 | ERR161320 |
| HVM3017 | ERR161328 |
| S122EC | ERR161285 |
| MS2481 | ERR161252 |
| S98EC | ERR161261 |
| S97EC | ERR161260 |
| S99EC | ERR161262 |
| S125EC | ERR161288 |
| S111EC | ERR161274 |
| S109EC | ERR161272 |
| S121EC | ERR161284 |
| S131EC | ERR161294 |
| S15EC | ERR161240 |
| S123EC | ERR161286 |
| S126EC | ERR161289 |
| S132EC | ERR161295 |
| S130EC | ERR161293 |
| S96EC | ERR161259 |
| S113EC | ERR161276 |
| S101EC | ERR161264 |
| S47EC | ERR161250 |
| S30EC | ERR161246 |
| S43EC | ERR161249 |
| B36EC | ERR161254 |
| S127EC | ERR161290 |
| S53EC | ERR161251 |
| S134EC | ERR161297 |
| S39EC | ERR161248 |
| S10EC | ERR161237 |
| S12EC | ERR161239 |
| HVM834 | ERR161317 |
| HVM1997 | ERR161322 |
| HVM1619 | ERR161321 |
| S133EC | ERR161296 |
| S124EC | ERR161287 |
| S129EC | ERR161292 |
| IR68 | ERR458473 |
| IR65 | ERR458472 |
| IR49 | ERR458471 |
| S93EC | ERR161256 |
| S1EC | ERR161234 |
| S11EC | ERR161238 |
| P189EC | ERR161314 |
| S92EC | ERR161255 |
| S117EC | ERR161280 |
| S116EC | ERR161279 |
| P146EC | ERR161313 |
| S95EC | ERR161258 |
| P56EC | ERR161310 |
| HVR2496 | ERR161326 |
| HVM5 | ERR161306 |
| HVM3189 | ERR161329 |
| P50EC | ERR161307 |
| HVR83 | ERR161311 |
| S100EC | ERR161263 |
| S110EC | ERR161273 |
| S102EC | ERR161265 |
| S112EC | ERR161275 |
| MS2493 | ERR161253 |
| HVM826 | ERR161316 |
| P53EC | ERR161309 |
| S135EC | ERR161298 |
| S107EC | ERR161270 |
| S108EC | ERR161271 |
Warning: The data is ~1GB.
Option 1) Download the current release as an archive:
With wget:
$ wget https://github.com/BeatsonLab-MicrobialGenomics/ST131_99/archive/1.0.tar.gz -O ST131_99-1.0.tar.gz
Option 2) Clone the current master branch in this repository:
Please ensure you have git installed. git can be really useful for scientists. See here for some discussion.
With git:
$ git clone --recursive https://github.com/BeatsonLab-MicrobialGenomics/ST131_99.git # The --recursive option is used to pull down all the smaller repositories
Programmatic Access:
If you're only interested in a subset of strains you should be able to write a curl or/wget call.
- The files have the following patterns:
- draft assemblies- https://github.com/BeatsonLab-MicrobialGenomics/ST131_99/blob/master/assemblies/$STRAINID_*_Contigs.fasta
- ordered assemblies against complete EC958- https://github.com/BeatsonLab-MicrobialGenomics/ST131_99/blob/master/ordered/$STRAINID_*_Contigs-against-EC958.fas
We updated VFDB in May 2014 to include the fimH, parC and gyrA alleles used in the study. Please see: https://github.com/BeatsonLab-MicrobialGenomics/VFDB/tree/master/fimH_parC_gyrA
These are the sequences along with the draft genomes that were used as inputs to SeqFindR to generate the presence/absence plots (Figure 3, Figure S4, and Figure S6). See the VFDB repository for more information.
- Contains:
- VFDB/ - Virulence factor & Islands sequences. SeqFindR formatted.
- assemblies/ - the assembled contigs from Velvet.
- ordered/ - the assembled sequences ordered against EC958. The complete EC958 genome can be downloaded from here.
The assembly statistics are provided. The draft assemblies were ordered with The Mauve Contig Mover (MCM).
The 99 ST131 genomes were analysed using the Banzai Microbial Genomics Pipeline. We also used the EasyFig, SeqFindR and BRIG tools developed within the Beatson Lab.