San Diego USA, the Poorly Assembled Genomes (PAG) meeting got off to an exciting start this year as a little know bioinformatics company ordasIT took centre stage having solved the age old ‘assembly problem’ with their new secret algorithm ‘DenovoHocusPocus’
Over the years scientists have been constantly frustrated by the fact that maths has stood in the way of getting a good assembly. Mike Devon, a Norfolk farmer and complex genomes specialist explained ‘we have been constantly told that genomes are fragmented because reads are short and repeats are long, therefore, because of something to do with maths, that biologists will never understand, we cant get long contigs just by sequencing more. It now turns out that the mistake we have been making has been that we have been over-thinking the problem”
Prof. Dumbledore, CEO of ordasIT and Head Wizard explained the DenovoHocusPocus methodology. “we observed that, historically, limitations imposed by physics have been overcome by using magic – so that’s the route we took here. However, people sometimes find the use of wizardry disturbing, so to help the end user we have made our entire assembly pipeline invisible”.
You cant run the ordasIT pipeline yourself as, to get around established mathematical theory, it must exist in a magical universe (a bit like Hogwarts). Instead you have to send your data to Dumbledore directly who, for a fee, will return a single contig per chromosome (or however many contigs you want).
Not all delegates at the PAG meeting were impressed, a sour faced delegate at the back of the room was overheard saying ‘this all smells like snake oil to me’, but nobody was listening and by that time Dumbledoor had left the building at high speed in his vintage Ferrari.