SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Help me if u can plz marinevikash General 3 04-04-2014 05:20 AM
Bowtie beginner question... milesgr General 6 03-14-2012 07:21 AM
Beginner Sequencing Analysis question mgibson General 0 06-17-2011 10:30 AM
1000 genomes - a beginner question EHC Bioinformatics 3 05-26-2011 01:51 AM
"beginner in alignment" question menenuh Bioinformatics 1 03-10-2010 10:57 AM

Reply
 
Thread Tools
Old 10-22-2011, 11:15 AM   #1
metaStudent
Junior Member
 
Location: London

Join Date: Oct 2011
Posts: 3
Default A real beginner's question on metagenomics! Plz help!

Hi, I'm very much new to the field of metagenomics and sequencing. I have been trying to find out answers for this but I haven't been too successful probably because the answer is too obvious or my understanding is completely plainly wrong... Anyway, it would be great if some of you could enlighten me with an answer!

In metagenomics, say a soil sample is taken for sequencing. Now, fragmented genomes from this mixture of species are sequenced say by 454 sequencing. My question is, will there always be some overlapping regions to guide de novo assembly? If I am understanding this correctly (probably not!), there will be abundant species in the sample and their genomes will be fairly easy to assemble as there are lots of them, but for the less abundant species, there won't be enough of them to have enough overlapping regions of the genomes for de novo assembly. I know this is a bit extreme, but what if there happens to be just one member of a novel species in the sample? is there just no way for the whole genome of this species to be sequenced?
metaStudent is offline   Reply With Quote
Old 10-22-2011, 09:42 PM   #2
rskr
Senior Member
 
Location: Santa Fe, NM

Join Date: Oct 2010
Posts: 250
Default

Maybe try assembling a couple polyploids with samples from various different strains of the same species, heck try assembling a single species from a single sample accurately, then figure whatever is in the meta soup is pretty close to nonsense alpha=.0001, especially after you take into account 454 is only accurate in high coverage regions and you probably only have at most a couple of 454 runs. So you might as well give up, or at least make up some results.
rskr is offline   Reply With Quote
Old 10-23-2011, 08:43 AM   #3
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Quote:
Originally Posted by rskr View Post
Maybe try assembling a couple polyploids with samples from various different strains of the same species, heck try assembling a single species from a single sample accurately, then figure whatever is in the meta soup is pretty close to nonsense alpha=.0001, especially after you take into account 454 is only accurate in high coverage regions and you probably only have at most a couple of 454 runs. So you might as well give up, or at least make up some results.
While this could've been said nicer (), I mostly agree. New species discovery by soil shotgun de novo sequencing is a hard problem.

Maybe with a few billion long reads....but i doubt with current technologies/throughputs. Either that or single cell sort + WGA + WGS.
ECO is offline   Reply With Quote
Old 10-23-2011, 02:03 PM   #4
metaStudent
Junior Member
 
Location: London

Join Date: Oct 2011
Posts: 3
Default

Thank you, but I'm sort of more confused...

My question was, will there always be some overlapping regions to guide de novo assembly even for those species which are less abundant in the sample?

Really sorry if I failed to understand your previous answers.
metaStudent is offline   Reply With Quote
Old 10-23-2011, 07:50 PM   #5
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

There will never always be anything in biology...

Your question is not really answerable with real facts, unless you already know how many species are present in your sample and at what abundances. It's a pretty easy calculation to estimate: how many species do you have, what are their relative abundances, how big are their genomes, how big is the insert size of your library, and how many reads will you generate. Of course there are more difficult questions of species similarity, repeat content, but the above is probably a good exercise for you to work through.

The conservative answer is (especially with a few million reads from a few 454 runs)...that you will not have enough coverage to de novo assembly an entire RARE organism out of a metagenomic pool, let alone be confident that any apparent overlap is biologically real.
ECO is offline   Reply With Quote
Old 10-24-2011, 03:33 AM   #6
metaStudent
Junior Member
 
Location: London

Join Date: Oct 2011
Posts: 3
Default

Thank you ever so much! I think all the confusion started when someone told me it's possible to conduct whole genome sequencing from a metagenomic soup! I suppose de novo sequencing in metagenomics is a dream that this stage! Thank you for your answers!
metaStudent is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO