New to sequencing and analysis

[new2sequencing]

Hello all!

I am new to genome sequencing and analysis. My lab recently got a bacterial genome sequenced from a company who sent us the files containing the results of the genome sequence. Now I am expected to analyse this genome. Can anybody guide thru the basic steps of sequence analysis.
As a first step, what should do with the sequence?

[Nomijill]

In response to New2Sequencing

Hi New2Sequencing -

Please excuse me if I tell you things you already know. I figure better that way than the reverse.

The type of analysis problem that you have depends on whether or not you have a reference sequence for your bacterial sequence. If you don't, then you need to do a de novo assembly. If you do, then you will want to map your reads to that reference. There are a lot of different tools available to perform these types of analyses. Because I work for CLC bio, I am most familiar with our tools, but many other sources, commercial and free, also provide tools for de novo assembly or reference mapping. SeqAnswers has a great list of these in their Wiki. The tool that you select will also depend on the type of reads that you have, long or short, color space or base space. The technology that was used to generate your data will answer these questions for you.

If you are interested, CLC's Genomics Workbench is free to try for two weeks, it is easy to use, and it has some nice tutorials to get you started. It is also convenient if you do not have access to powerful computers, because it uses compute resources very efficiently. I just read a blog from Nick Loman on a de novo assembly of E.coli that was generated with Ion Torrent. He was able to assemble the entire genome, 49Mb of data for 10x coverage, in less than two minutes on an 8g desktop. Other assemblers took days. CLC bio may not be the solution you end up with, but it is a really sweet place for a beginner to start. I hope it helps you.

[krobison]

Start by finding & reading about 10 recent publications which are closest to your research project; this give you a feeling for some typical analysis strategies, but also the sorts of questions which are being asked.

Of course, in the end the real question is "what question(s) do I want to know the answers to?". Why did your boss decide to sequence the organism(s) in question? Defining that in detail will drive the analysis.

[new2sequencing]

Thanks Nomijill: that was helpful. Now I will start reading about de novo assembly and try out the softwares/freewares u mentioned. Will keep all posted.

@krobison: That is an important suggestion. I have started reading a book about genome sequencing, however it is taking time. i should simultaneously start reading the papers.

Trying to answer your 'why' question: I think we isolated a unique biofuels producing bacteria that showed phylogenetic similarities (16s rRNA sequencing) to a previously known bacteria, however some of the properties of the new bacteria are very unique and hence the sequencing was done. Ours is more of gaining incremental knowledge !