-
Notifications
You must be signed in to change notification settings - Fork 17
Sequence reads
- Ion Torrent: BGI have released 7 x 314 chips of Ion Torrent data, available from ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482.
- Illumina fragment: BGI have also sequenced TY2482 to >200x coverage using Illumina (confirmed) ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/110601_I238_FCB067HABXX_L3_ESCqslRAADIAAPEI-2_1.fq.gz
- Illumina paired-end: BGI have sequenced TY2482 with paired-end Illumina but data not released (although an assembly incorporating these reads available)
Life Technologies and University Muenster have released eight 314 chips worth of reads for the outbreak strain, LB226692. The FASTQ files are avaialble at http://www.iontorrent.com/applications-speed/. SFF files are available at http://lifetech-it.hosted.jivesoftware.com/docs/DOC-1518
Health Protection Agency have released a 2x8kb Paired End and 2xShotgun sequence of outbreak strain H112180280 sequenced by 454. The 13 scaffold asssembly and an annotated genbank file are available for download at http://www.hpa-bioinformatics.org.uk/lgp/genomes. The sff file was originally uploaded but no longer available. On June 20 they also released Illumina MiSeq data (read & assemblies) for this strain and 4 others, also available at http://www.hpa-bioinformatics.org.uk/lgp/genomes
Göttingen genomics laboratory has sequenced two isolates of the E.coli O104:H4 outbreak strain on a Roche 454 sequencer. german website
Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer F-D, Boelter J, Petersen H, Gottschalk G, and Daniel R (2011). Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Archives of Microbiology (accepted).
Sequencing data is available via FTP:
- ftp://ftp.g2l.bio.uni-goettingen.de/
- User: EAHEC_GOS
- Passwort: EAHEC_GOS
Pacific Biosciences completed a de novo sequence assembly of the Escherichia coli O104:H4 strain responsible for the recent outbreak in Germany and sequenced 11 related bacterial strains (including 6 previously unsequenced strains of the same serotype) for comparative analysis.
Sequencing data available at http://www.pacbiodevnet.com/share/datasets/ecolioutbreak
This strain, isolated in 2001 is the same MLST type as the 2011 outbreak strain and carries the STX2 locus. For further details see:
Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. (2011) Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. PLoS ONE 6(7): e22751. (http://dx.doi.org/10.1371/journal.pone.0022751)
Sequence read data is available at http://lifetech-it.hosted.jivesoftware.com/docs/DOC-1835. (Registration is required but permission is granted immediately following registration).