Archive | March 2015

Is perfect genome assembly possible? Yes, says Gene Myers.

According to Gene Myers (near) perfect genome assembly is within reach for any organism of your choice.

Time will tell if he’s right, but being an influential bioinformatician who has made key contributions in sequence comparison algorithms such as BLAST, whole-genome shotgun sequencing and genome assembling, one will think he knows what he’s talking about!

shotgun sequencing

Shotgun sequencing, Adapted from Commins, J., Toft, C., Fares, M. A. – “Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects.” Biol. Procedures Online (2009). Accessed via SpringerImages. CC BY-SA 2.5

In a conference at the PRBB auditorium today, he explained to a mixed audience of biologists and computer scientists how, after a few years dedicated to other issues (mostly image analysis), he was now coming back to sequencing with great excitement. The reason: PacBio RSII. This sequencing device is able to produce very long reads (of more than 10,000bp!) and has a couple of other characteristics that can potentially make full assembly possible: although error rates are high (10-15%) they are random, not like with other techniques that tend to make always the same errors. And sampling is also random. This randomness and the length of the reads mean that, with enough sequencing coverage, you can always get the right sequences.

So now all we need, Myers says – apart from waiting for the cost of the PacBio to go down, which he promised will happen soon (4x in one year) – is to build an efficient assembler. He talked about what he and some colleagues have been doing in that sense. The main element is a ‘scrubber’ to clear and edit the reads while removing as little data as possible. Because his point was that even though people have been focusing on the assembly, the real problem is the data, the contaminants, chimeras, excessive error rates,… So he presented his personal ‘data cleaner’, DAscrub, soon to be released.

You can read more details about his recent work on this in his blog,

In the meantime, his advice to the world – stop the 10,000 genomes project right away and wait a couple of years to have better sequences!

Share your #passion4science!

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Do you love science? Do you remember what made you decide to become a researcher? Was it a person you met, a movie you watched, a book you read, anything special that happened to you as a child? Were you 16, or 12? 8? 4?

Whatever it was that sparked your passion for science, share it with us – your story may inspire young people to start their path in this exciting career!

At the PRBB we are organising “BioJúnior” for next April 17 – an event aimed at young students who are about to embark on their career journey. We are trying to collect as many anecdotes, experiences, reasons or feelings as possible to help spark their interest in science and research. Will you help us?

Just tell us your story. You can do so via Facebook, Twitter or Google+, tagged #passion4science. You can write it in English, Catalan or Spanish.

All comments received will be used during the students event, as well as further shared with the world through social media or other means*. So don’t forget to share your experience – and do share this message with all your peers!!!

*All information submitted through the #passion4science campaign, including your name, may be shared through the PRBB social networks or by other means, always under a Creative Commons BY-NC-SA 3.0 license.

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