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Tag Archives: minION
Real-time phylogenomics or ‘Some interesting problems in genomic big data’
Talk given at a technology/informatics company, London, Feb 2018. An overview of contemporary advances and remaining problems in big-data biology, especially phylogenomics. Tweet this Digg Post to LinkedIn Slashdot Stumble This
Posted in Publications, Science, Talks
Tagged citizen-sequencing, DNA sequencing, genome cosmology, informatics, minION, nanopore, phylogenomics, real-time phylogenomics
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Tent-seq: the paper (aka ‘field-based, real-time phylogenomics’)
Really proud to report that the first of our bona fide real-time phylogenomics papers is now out in Scientific Reports! In the paper we managed to show a number of things that are potentially really exciting, and I’ll get to … Continue reading
Posted in Science
Tagged bioinformatics, blast, field-based, minION, phylogenomics, real-time, real-time phylogenomics, sequencing
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What is ‘real-time’ phylogenomics?
Over the past few years I’ve been developing research, which I collectively refer to as ‘real-time phylogenomics’ – and this is the name of our mini-site for MinION-based rapid identification-by-sequencing. Since our paper on this will hopefully be published soon, … Continue reading
Posted in Science
Tagged data, minION, nanopore, phylogenomics, phylogeny, real-time phylogenomics
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Some aspects of BLASTing long-read data
Quick note to explain some of the differences we’ve observed working with long-read data (MinION, PacBio) for sample ID via BLAST. I’ll publish a proper paper on this, but for now: Long reads aren’t just a bit longer than Illumina data, … Continue reading
Posted in Coding, Science
Tagged blast, long-read, minION, nanopore, pacbio, real-time phylogenomics
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More MinION – the ‘1D rapid’ prep
My last MinION post described our first experiments with this really cool new technology. I mentioned then that their standard library prep was fairly involved, and we heard that the manufacturers, Oxford Nanopore, were working on a faster, simpler library prep. We … Continue reading
Posted in Science
Tagged DNA sequencing, fungarium, Kew, minION, rapid sequencing kit, real-time phylogenomics
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Copying LOADS of files from a folder of LOADS *AND* LOADS more in OSX
Quick one this, as it’s a tricky problem I keep having to Google/SO. So I’m posting here for others but mainly myself too! Here’s the situation: you have a folder (with, ooh, let’s say 140,000 separate MinION reads, for instance…) … Continue reading
Messing about with the MinION
Molecular phylogenetics – uncovering the history of evolution using signals in organisms’ genetic sequences – is a powerful science, the latest expression of the human desire to understand our common origins. But for all its achievements, I’d always felt something … Continue reading