Hyde is a brazen two-column Jekyll theme that pairs a prominent sidebar with uncomplicated content. It’s based on Poole, the Jekyll butler. Built on Poole Poole is the Jekyll Butler, serving as an upstanding and effective foundation for Jekyll themes by @mdo. Poole, and every theme built on it (like Hyde here) includes the following: Complete Jekyll setup included (layouts, config, 404, RSS feed, posts, and example page) Mobile friendly design and development Easily scalable text and component sizing with rem units in the CSS Support for a wide gamut of HTML elements Related posts (time-based ..read more

I am just writing a short presentation for a meeting in Hinxton. I wanted to demonstrate the profound effect that whole-genome sequencing is having on the study of biology, and the size and scope of recent studies. So I thought it would be fun to catalogue the largest - in terms of samples - genome projects that have been published so far. A few things are notable here. As expected, many of the biggest studies in terms of numbers are bacterial, enabled partly due to their smaller genome size. Update: My attention has just been drawn to a study of 2,007 C. elegans genomes! I found it interestin ..read more

Wow, so last Wednesday we held the fourth instalment of our Balti and Bioinformatics series which was a brilliant success, attracting over 100 participants. The idea of this meeting is to bring those developing cutting-edge bioinformatics methods together with those who actually use them. Thanks to the generous sponsorship of the Centre for Genomic Research at the University of Liverpool and the Medical Research Council and the BBSRC we were able to change up a gear, inviting two incredible international speakers: Sébastien Boisvert and Daniel Huson. We were also able to afford a proper l ..read more

I help out with a fair few workshops on genomic analysis, but most are limited by being restricted to just a day or two, hardly enough time to cover more than the basics. So the 10 day long NERC Population and Metagenomics Analysis course, organised by the fantastic Konrad Paszkiewicz from the University of Exeter is a quite amazing opportunity. The teaching will be from some of the best people in the field (and me!) and of the highest quality. Incredibly, if you are a UK-funded researcher the costs of the course are entirely waived, with accommodation and meals also included! Spaces ..read more

  If you do Illumina sequencing you probably hear the words 'phasing' and 'pre-phasing' pretty regularly, but what does it mean exactly and why is it important? Well, with MiSeq read lengths now at 300 and HiSeq high-throughput mode soon to be 125, keeping phasing and pre-phasing levels under control will become increasingly important. Nothing can bring down a long read like high phasing or pre-phasing, and throwing higher densities into the mix only makes the problem worse. Here is a quick guide to troubleshooting high phasing and pre-phasing issues. What is phasing? In sequencing-by-s ..read more

I just got back from a short meeting in the States. Even though I was only out of the office a few days, I am now even further behind with backed-up peer review, finishing manuscript drafts, collaborations. My long-suffering family now have to cope with me being tired and irritable while I catch up on missed sleep and adjusting back to local time. And I can see several more weeks out of the office coming before Christmas. During the meeting dinner I fell to discussing the pressures of attending all these meetings and keeping sane with Julie Segre, an investigator at the NIH. It was great ..read more

You can use MEGAN to import TAB files exported by USEARCH, but only if you use USEARCH in local mode, as otherwise you don’t get e-values which MEGAN doesn’t like, e.g.: ./usearch7.0.1001_i86linux32 -usearch_local {}.fasta -db refs/SSURef_111_NR_tax_silva.udb -id 0.9 -blast6out {}.m8 -strand plus -maxrejects 0 -maxaccepts 0 USEARCH 32-bit mode (the free version) has a 4GB memory limit, which later versions of SILVA can exceed. SILVA 111 NR fits within 2B. MEGAN has a SILVA to GI lookup file, but this is only for version 108 of SILVA. Not clear how to make your own one from ARB files w ..read more

There have been rumblings of news from Oxford Nanopore at the American Society of Human Genetics meeting taken place at the moment in Boston. I have to admit I may have had advance sighting of their exciting press release today, leading to some very childish "I have a secret" type tweets between myself and a few others in the know! Luckily it is a secret no more. Today's announcement of the MinION access programme (MAP) is very exciting! For a refundable deposit of $1,000, Oxford Nanopore say - if you are selected - they will send you a MinION and a regular supply of flow cells "sufficient to ..read more

So far we have held three meetings in the Baltis and Bioinformatics series, which has had some great talks and resulted in some great connections being made. The meetings are based around the linked topics of genome sequencing and bioinformatics, with the idea to take leaders in the bioinformatics field, and put them together with students, post-docs, 'service' bioinformaticians and others at the coal-face of data analysis. The meetings should stimulate discussion, collaboration opportunities and learning. We traditionally finish off with a bioinformatics clinic, where you can ask the hardest ..read more

Another job ad! I'll try and post some original content soon. This is an opportunity to post-doc with Chris Quince, one of the smartest mathematical modellers working on genome and metagenome data 'in the game' (and also my mentor). Apply now (after reading the job description) ! Research Associate Bioinformatics for integrating polyomics data from synthetic microbial communities University of Glasgow -School of Engineering Ref: 004600 Salary: Grade 7, £32,267 - £36,298 per annum The University of Glasgow is embarking on an ambitious 5-year project, funded by an EPSRC Frontier Engineering Awar ..read more