Web-services

GoSeqIt offers web-services that based on DNA sequences enable fast, reliable, confidential, and user-friendly characterisation of bacteria.

The GoSeqIt Tools web platform is currently in public beta mode. This means you can sign up and try the platform for free.

When uploading bacterial draft genomes to GoSeqIt Tools, you will get information on:

  • The quality of the bacterial genome
  • The bacterial species (1)
  • The Multilocus Sequence Type of the bacteria (2)
  • Presence of acquired antibiotic resistance genes (3)
  • Presence of virulence factors (for Escherichia coliStaphylococcus aureus, Enterococcus, and Listeria) (4)
  • Presence of plasmids (for Enterobacteriaceae and gram-positive bacteria)  (5)
  • and finally plasmid Multilocus Sequence Typing for plasmids of the type IncN, IncHI1, IncHI2, IncI1, IncF and IncA/C (5)

Please click here to try GoSeqIt Tools: GoSeqIt Tools

The Bacterial Analysis Pipeline (6) and the E. coli serotyping (7) methods are now available via Illumina BaseSpace Sequence Hub.

References

1.

Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. Benchmarking of methods for genomic taxonomy. J Clin Microbiol. 2014 May;52(5):1529-39. PMID: 24574292. [PubMed] [Read by QxMD]

2.

Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012 Apr;50(4):1355-61. PMID: 22238442. [PubMed] [Read by QxMD]

3.

Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012 Nov;67(11):2640-4. PMID: 22782487. [PubMed] [Read by QxMD]

4.

Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014 May;52(5):1501-10. PMID: 24574290. [PubMed] [Read by QxMD]

5.

Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903. PMID: 24777092. [PubMed] [Read by QxMD]

6.

Thomsen MC, Ahrenfeldt J, Cisneros JL, Jurtz V, Larsen MV, Hasman H, Aarestrup FM, Lund O. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance. PLoS One. 2016 Jun 21;11(6):e0157718. PMID: 27327771. [PubMed] [Read by QxMD]

7.

Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015 Aug;53(8):2410-26. PMID: 25972421. [PubMed] [Read by QxMD]