Microbial
Cases
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Microbes make up the majority of the earth's biomass and have evolved for over 3.8 billion years. Knowledge of the enormous range of microbial capacities can have far-reaching implications for health, environment, energy, and industrial applications. With our NGS platforms and bioinformatics experience, BGI provides cost-effective services and fast turnaround time for sequencing microbial genomes. To date, BGI has sequenced 1,710 bacteria, 208 fungi and 2665 virus genomes using multiple technologies – Ion Torrent, HiSeq 2000 and Opgen.

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4. The New England Journal of Medicine. 27 Jul 2011.

Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid, bench-top DNA sequencing technology, open-source data release, and prompt crowd-sourced analyses. In less than a week, our studies revealed that the outbreak strain belonged to an enteroaggregative E. coli lineage that had acquired genes for Shiga toxin 2 and for antibiotic resistance.

Bioinformatics:

Bacteria re-sequencing
  1. Adaptor, contamination and low-quality reads filtering
  2. Reads statistics and quality control
  3. Survey assembly of bacteria and assembly optimization
  4. Single base depth and coverage analysis
  5. Variation analysis
  6. SNP calling, annotation and statistics
  7. InDel calling, annotation and statistics
Fungal re-sequencing
  1. Adaptor, contamination and low-quality reads filtering
  2. Reads statistics and quality control
  3. Single base depth and coverage analysis, consensus sequences, SNP calling, annotation and statistics
  4. InDel calling, annotation and statistics
  5. Structure variation（SV）detection and statistics (for your reference only)

Sample Requirements:

For the genomic DNA samples you provide us:
  1. Purity: OD260/280=1.8-2.0
  2. Concentration: ≥50 ng/μl
  3. DNA amount: single library preparation starts from at least 5ug, and the total amount should be determined case by case.

Technologies