Making genome assemblies in the year 2014

I often like to encourage students to explain their work without using any complex scientific vocabulary. If you can explain what you do to your parents or grand-parents then this is great practice for explaining your work to other scientists from outside your field.

I also encourage students to think of analogies and metaphors for their work as these can really help others to grasp difficult concepts. Yesterday, I wrote a post called Making cakes in the year 2014 which was (hopefully) an obvious attempt to explain some of the complexities and problems inherent in the field of genome assembly.

It almost feels wrong to even attempt to convert millions of ~100 bp DNA fragments into — in the case of some species — a small number of sequences that span billions of bp. Every single step in the process is fraught with errors and difficulties. Every single step is controlled by software with numerous options that are often unexplored. Every single step has many alternative pieces of software available.

If we just focus on one of the earliest steps in any modern sequencing pipeline, the need to remove adapter contamination from your sequenced reads. There are at least thirty-four different tools that can be used for this step and there are over 240 different threads on SEQanswers.com that contain the words 'trim' and 'adapter' (suggesting that this process is not straightforward, and that many people need help).

I had a look at some of these tools. The program Btrim has 12 different command-line options that can all affect how the program trims adapter sequences (it has 27 different command-line options in total). Skewer has 9 different command-line options that will affect the output of the program. The trimmer Concerti has 8 options that will also affect the output. Do we even have a good idea of what is the best way to remove adapter sequences? Maybe we need a 'trimmathon' to help test all of these tools! 

If there is a point to this post maybe it would be that genome assembly is an amazingly complex, time consuming, and fundamentally difficult problem. But even the 'little steps' that that have to be done before you even start assembling your sequences are also far from straightforward. Don't convince yourself for a moment that a single tool — with default parameters — will do all of the hard work for you.

 

 

PLOS Computational Biology: Ten Simple Rules for Writing a PLOS Ten Simple Rules Article →

Is there practical advice for contributing to the Ten Simple Rules collection already available? What can we learn from the existing articles in the collection? If only there was an article with ten simple rules for writing a PLOS Ten Simple Rules article. If only that article could be peppered with insightful comments from the founder of the collection: Philip E. Bourne.

This is that article.

This is very meta. I think I will wait for the 'Ten Simple Rules for Writing a Ten Simple Rules Article about writing a PLOS Ten Simple Rules Article'.

Making cakes in the year 2014

I've been trying to make a cake. There are lots of published recipes out there for how to make this cake, but the one that I used came with only a very blurry image of what the finished cake should look like. So I really had to hope that the recipe was a good one, because I wasn't entirely sure if I would be able to tell whether it worked or not.

To get started, I used one of those online shopping services that can deliver all the ingredients to your door. Even though they claimed that they stocked everything on my shopping list, they then informed me that there were a small number of ingredients that they were not able to physically access at the moment. Frustratingly, they weren't able to tell me which ingredients would be missing when they delivered them. How odd. 

Something else that seemed unusual was that my cake recipe specified that I needed almost 100 times the amount of ingredients compared to what will end up in the finished cake. Seems a bit wasteful, but who am I to argue with the recipe?

Before I could actually start the baking process, I found that there were a few issues that I had to overcome. Lots of the ingredients had become stuck to the packaging and I had to use a tool which could separate the two. Only, some of the time it didn't get rid of all the packaging, and some of the time it ended up getting rid of not just the packaging but some of the ingredient as well. There's actually several tools on the market for doing this, but they all seem to perform slightly differently.

After I got rid of the packaging I noticed that lots of the ingredients had started to spoil and had to be thrown away, but some of them could be salvaged by cutting off the bad parts. There also seemed to be a lot of implements that you can buy to help with the cutting. Wasn't obvious which one was the best, so I used the first one that Google suggested.

At this point it was kind of frustrating to notice that a small proportion of my ingredients weren't cake ingredients at all. I had to throw them all away, but I think that some of them may have ended up in the final cake.

When it came to the actual baking, I was a bit overwhelmed by the fact that there were dozens of different manufacturers who all claimed that I could make a better cake if only I used their brand of oven. Nearly all of these ovens just let you put your raw ingredients in one slot — after you have removed packaging, the spoilt ingredients, and the non-cake ingredients — and voila, out comes your cake!

I chose one of the more popular ovens on the market and waited patiently for many hours as my cake baked happily in the oven. When the timer buzzed and I took the cake out, I was surprised to that many of the raw ingredients were left behind in the oven's 'waste overflow unit'. The real surprise however, was that the finished cake didn't really look anything like the — admittedly blurry — photo that came with the recipe. 

The cake had many different layers, but they weren't quite all the same size and some of them seemed to have been assembled in the wrong order. The pattern on the cake decoration — yes this oven also decorates the cake — was inconsistent at best. It would mostly use one color of icing, but every now and then, it would insert a different color. The same thing happened with the fillings, it would randomly switch from one flavor to another, and then back again. It was almost like there were two different cakes which had  been squished together to make a new one.

When I finally showed the cake to one my baking friends, I was hoping that he would enjoy it. However, all he kept asking me was "How big are the layers?". When I told him, he replied "My cake has bigger layers so yours can't be very good", and then he left. How rude. I took it to another friend and she just said "Your cake is smaller than mine so mine must be better". She also left without trying it. Finally, I took it to another baking colleague. Before I could show him the cake he just said "My cake has most of the common ingredients expected in all cakes, how many does yours have?". I didn't know so he left.

Making cakes is a very strange business.

How would you pronounce the name of this bioinformatics tool?

From the latest issue of Bioinformatics we have a new tool that is an R package for the analysis of GWAS studies. Rather than name the tool, I want you all to first see it exactly as it appears in the journal:

The first character in the name of this software is a character which can often be hard to identify, particularly when certain fonts makes it look like it could be the letters L or I, or even the number 1.

This is not a name that is worthy of a JABBA-award, but it does fall in to my category of posts which I call almost JABBA, for software names that have various other issues. The particular issue in this case is that the name is hard to read and therefore hard to pronounce. I feel that the use of lower-case characters makes it more likely that the reader will attempt to pronounce this as a word, rather than read it as an initialism. E.g. maybe you saw this name and read it as 'Lurgpurr', or 'Ergpurr'.

The reason behind the name is not explained in the article, but when you go to the linked software page, all is revealed:

It's a bit odd that one of the five words that appear in this name ('Gaussian') doesn't get mentioned anywhere in the paper. But more importantly, why did they feel the need for using lower-case characters? 'LRGPR' would have been much easier to read and comprehend than the font-dependent 'lrgpr'.