Should you buy a nanopore sequencer?

This morning twitter is awash with posts discussing the newly announced nanopore sequencers from Oxford Nanopore. Speculation has been rife for some time about the potential specifications of the first sequencers to be produced by the company, and it certainly appears that the company have fulfilled the expectations placed upon them. I’m not going to…

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Published:February 18, 2012 View Post

Bioinformatics Technology

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Review of Hanson SB5 Baritone Saxophone

Background Hanson music wasn’t a name I’d seen before I saw an advert for one of their baritone saxes on Ebay. I’d normally be wary of buying an unknown brand of sax over the internet, but there was one thing which piqued my interest.  Most companies have a selection of favourable customer comments on their…

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Published:February 12, 2012 View Post

Music

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The true cost of object creation in java

I’ve been spending some time trying to optimise the data loading part of one of my java projects.  The nature of the data we use means that we have to create hundreds of millions of objects, each of which internally stores only a single long value (it actually stores several fields packed into this value…

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Published:December 6, 2011 View Post

Computing

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Moving over to Casava 1.8

Introduction Illumina have recently released an updated version of their downstream analysis software CASAVA.  This is the analysis pipeline which runs after the sequencer has processed the raw data down to base call files and provides a variety of functionalities from creating usable base calls to alignment and variant calling.  Casava 1.8 makes some major…

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Published:September 16, 2011 View Post

Bioinformatics Computing

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Importing RNA-Seq data into SeqMonk

Introduction Mapped RNA-Seq data coming from eukaryotes is probably the most complicated data type to import into SeqMonk due to it’s relative complexity and the abundance of options with which you are presented.  Depending on exactly what sort of information you want to know about your data different data import options will be useful, so…

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Published:September 4, 2011 View Post

Bioinformatics

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Getting the java heap size you asked for

In a recent post I discussed a method we’re using for automatically setting the java heap size appropriately at runtime. It now turns out that the issue of setting the heap size is complicated by the fact that the heap size you request on the command line isn’t necessarily what you get given. In some…

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Published:August 26, 2011 View Post

Computing

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Mac application bundle caching

Having spent a frustrating hour or so trying to update a mac application bundle I thought I’d share a couple of things which caused no end of confusion and aren’t what you’d expect and are therefore likely to catch out those working with application bundles for the first time. Basically I was finding that although…

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Published:August 10, 2011 View Post

Computing

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Dynamically setting the java heap size at runtime

One of the oddities about java programs is that they require you to set a maximum heap size when you start the program. What this means in effect is that you need to be able to predict the memory usage of your program before it starts, and whatever heap size you set needs to be…

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Published:July 29, 2011 View Post

Computing

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Want to improve your science? Get a dog.

Actually the dog is somewhat irrelevant – it’s what comes with it which matters.  One of the side-effects of dog ownership is that you get to spend an hour or so a day out walking, which means you have an hour or so with your own thoughts and no distractions. I’m sure everyone has experienced…

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Published:June 19, 2011 View Post

Bioinformatics Computing

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Choosing the best format for raw sequence data

Introduction In the current Illumina pipeline raw sequence data is generated in qseq files, but can optionally be converted to the more standard FastQ format for use with other analysis programs.  The FastQ files produced are uncompressed text files and take up a considerable amount of space in our storage system.  We’ve therefore been thinking…

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Published:June 16, 2011 View Post

Bioinformatics Computing

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