Doing whole genome sequencing on a plant. Used nanopore reads and currently assembling plastid genomes and then will use Amazon AWS to do the nuclear assembly. Largest computational project Ive done thus far. Bioinformatics has become the cornerstone of my research effects in my home lab.
On May 25, 2017 3:40 PM, "Tom Randall" <tarandall@gmail.com> wrote:
The most sophisticated is using standard assemble to reference tools within Galaxy for a fungal genome that I had MWG Operon sequence for me on an Illumina HiSeq machine. See about halfway down this page for a brief description.--
http://roningenetics.org/Sequencing.html
Tom
On Tuesday, May 23, 2017 at 4:45:46 PM UTC-4, Patrik D'haeseleer wrote:Hoping for some quick feedback - How much use to people at your community lab make of bioinformatics? What is the most sophisticated piece of computational work you've done so far?At Counter Culture Labs, we have someone doing molecular dynamics simulations for protein linker design. And at BioCurious, we mined some Arabidopsis gene expression data to design novel spatiotemporal promoters. That's about the most sophisticated we've done so far. Other than that, it's mostly some Blast, primer design, codon optimization etc - nothing fancy.I've been asked to be on a National Academy of Sciences panel this Thursday about synbio and DIYbio (together with Drew Endy, and Tom Burkett from BUGSS), and I'm supposed to talk about how computational tools are enhancing ease of use in DIY labs. Figured I'd do a quick poll of the rest of the community...Thanks!Patrik
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