SPEEDY DE NOVO ASSEMBLY OF MICROBIAL GENOMES
Microbes play an important role in the growth and development of plants. Both as pathogens or beneficial microbes. Spadix offers several plant micro-organisms identification and -characterization services. In collaboration with our technology partner Future Genomics Technologies we now offer for our clients in agriculture an ultrafast (one business day) and accurate (>99.5% accuracy) identification of complete microbial genome sequences.
Specifications of a case study
- Bacterial strain: Escherichia coli K12
- Input: 2 mL stationary overnight culture
- DNA yield: ~2 µg HMW gDNA
- Platform: NGS based Long Read Sequencing
- Raw data yield: 800 Mb (fastq format)
- Bioinformatics: de novo contig assembly and 2x contig correction
- Product: 1 contig of 4,64 Mb with 99.72% identity to reference (4,64 Mb)
- Optional polishing toward qv>40
Total duration of pipeline: 6 hours
Vacancy Intern Bioinformatician (fulltime)
Spadix, founded in 2018, is a contract research laboratory specialized in genomic research. We offer a wide range of Next Generation Sequencing services for the plant breeding industry. Our services include genomics, transcriptomics, marker assisted breeding technologies, quality control services and bioinformatics. Spadix is located at the Bio Science Park in Leiden, the Netherlands.
About the position
Due to our continued growth we have an exciting opportunity for a highly motivated Intern Bioinformatician willing to work on the development of a Bioinformatic pipeline supporting one of Spadix’s technology platforms.
We are looking for
A highly driven motivated candidate with knowledge of Python, Linux and NGS technologies. Additional knowledge of or feeling for plant genomics, Perl, R, distributed source code version control systems (Git or Mercurial) are of benefit.
As an Intern Bioinformatician you are amongst others responsible for the development of an analysis pipeline needed to support one of Spadix’s technology platforms.
- BSc/MSc student in bioinformatics or related study
- Available for a period of 5-9 months
- Feeling for pipeline development
A challenging fulltime position in a young and growing high tech company. Internship compensation depends on the qualification of the candidate.
Apply before June 30, 2020
Where to meet us?
Spadix is present at important plant breeding and genomics conferences. Below is an overview of events where you may meet us.
- January 12-16, 2019 Plant & Animal Genome Conference