[mira_talk] Re: mira- assembly jobs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 5 Mar 2011 17:11:02 +0100
On Wednesday 02 March 2011 12:42:58 Visam Gültekin wrote:
> [...]
> I am wondering what are the basic steps of this area, what kind of
> instructions to follow, etc..? There are so many questions and most of
> them should be answered by my own effort of course, but where to dig to
> find the treasure?
Actually an intersting question, I had hoped a couple of other people to come
forward to say how they learned stuff about this topic. As no one else does,
I'll start. But please be advised that part of the following is just a
personal opinion.
> I am trying to read articles about the topic i am asking, but there are so
> many gaps. One tells about north, another from south. There might be some
> cookbooks, some recipes that can be followed i think.
Well, you basically hit the nail on the head with that observation: like
cookbooks, recipes for sequence assembly come in tons of different flavours and
there are a multitude of them. Unfortunately, unlike cookbooks, many of the
underlying technologies change so rapidly that recipes which were valid 15
years ago (or sometimes 10 or even 5) are simply not valid anymore.
When trying to get into this field, its technologies and methods to tackle the
data coming from them, then your best option is to actually work together with
people who run a sequencing lab. They'll know the ins and outs and will be
able to provide you with literature which is not open to the public (vendor
documents often are not ... for whatever reason). And it's still interacting
with people you'll learn most.
If you do not have such a link, then things get more difficult. Your first stop
then are the technology vendor sites (454, Illumina, Pacific BioScience) who
have some general info regarding their sequencing technology.
Your second stop: http://www.sequanswers.com/
It has developed to be a must read for everyone in the sequencing area. Tons
of question with an equal amount of answers ... many of them even quite good
as from knowledgable people. What you first should do is simply selectively
read postings from the last two or so years (reserve some time for that). A
couple of things should be clearer to you then.
Afterwards, fell free to ask the very same question also on the SeqAnswers
board. Because I think that having a sticky post there tackling this kind of
information would be useful.
B.
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