Partnering opportunity

Bioinformatics polishing service for pacific biosciences sequencing of microbial genomes

Summary

A Spanish biotechnological institute offers its bioinformatics service for the polishing of pacific biosciences sequencing assemblies in order to obtain a more accurate genome sequence. Biotech companies and academic researchers are sought for services agreements.

Partner sought

Biotech companies, academic research groups and any other organization interested in the study of microbial genomics (industrial microorganisms, high-producer mutants, pathogens and other bacteria) are sought in order to established a service agreement.

Description

The organization is a Spanish biotechnological private non-profit research institute, founded in 1993, whose main activities are related to molecular biology and microbial biotechnology. The institution keeps close links with industrial research and innovation. The team covers several techniques and counts with a long experience in scientific research in European funded projects. High-throughput sequencing technology has allowed to obtain quite easily the whole genome sequence of any microbial organism. The different platforms can be divided in two groups: those that provide short but accurate sequence reads and those that provide long reads, but with much higher error rates. Most sequencing projects have employed short read technology; despite of the higher accuracy, the shorter reads cannot resolve repetitive stretches that are present abundantly in most genomes. As a result, the assemblies of the reads are composed of shorter contigs and a large number of them. Moreover, the repeat sequences, that often play important biological roles, remain unknown in terms of their exact sequence and genome location. Pacific biosciences (PacBio) is one of the long-read sequencing technology currently available, and has been commercially available since 2011. Because of its relative long presence in the market it is an established and stable platform which also includes advanced bioinformatics software. Most PacBio sequencing services provide, not only the sequencing reads, but also an automatic sequence assembly through its bioinformatics service. This first assembly can be polished using advance software that corrects the erroneous sequences of the reads taken into account the sequence from tens of aligned reads. The final output is a more accurate sequence. However, this software is difficult to install and use. Thus, the bioinformatics services are offered in order to polish microbial genome assemblies. Biotech companies interested in the study of microbial genomics as well as academic research groups can benefit from the bioinformatics polishing service for pacific biosciences sequencing of microbial genomes thought services agreement.

Advantages and innovations

The institute counts with a long experience in molecular microbiology and omics techniques. The expertise in dealing with genome projects of microorganisms of complex sequences, such as actinomycetes (high gas chromatography content, repetitive sequences and large genomes) is an advantage of the bioinformatics service. The software used for polishing is provided free from PacBio, however, the service will avoid the custom researcher to avert the complex installation and use of the polishing software, as well as the evaluation of the results.

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