SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
Miseq - Bacterial WGS at depth of 10 fold vl80 Illumina/Solexa 4 06-25-2013 04:44 PM
Ion Torrent $1000 Genome!? Benchtop Ion Proton Sequencer aeonsim Ion Torrent 88 10-28-2012 05:50 AM
Ion Torrent Protocol? PersianExcurzion Ion Torrent 25 02-15-2012 08:39 PM
Multiplexing with ion torrent? singaporeseq Ion Torrent 3 11-30-2011 08:49 PM
ion torrent herrroaa Introductions 5 07-25-2011 06:36 AM

Reply
 
Thread Tools
Old 06-25-2013, 07:20 AM   #1
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default Ion torrent: bacterial WGS coverage

Hi all,

I am new to ion torrent.

We are interested in getting the bacterial whole genome sequencing( ~2MB )...

However, i am not sure what is the coverage/depth we need to use to get the good read quality and assembly.

Can anyone help me out with this

regards

rosh
roshanbernard is offline   Reply With Quote
Old 06-25-2013, 08:37 AM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

De novo or resequencing?

Probably shoot for >50X coverage minimum. Higher initial coverage will allow more aggressive trimming/filtering of reads.

I have not assembled Ion data for a while, but historically the homopolymer calling issue leads to assemblies rich in indels. Perhaps someday someone will write the equivalent of Quiver for Ion Torrent data, but that hasn't happened yet.

Quality of the assembly will also be significantly affected by GC content (expect issues in regions with extremes in GC content) and the nature of the repeats in the genome. Set your expectations appropriately; short read, short insert technologies such as Ion cannot routinely close bacterial genomes -- you need either very long reads (PacBio) or mate pairs to have good odds of doing that.
krobison is offline   Reply With Quote
Old 06-25-2013, 04:47 PM   #3
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

ah okie... previously we have used the illumina reads. this is the first time we are going with ion torrent. anyways lets hope for the best.. i am planning to go with 35 to 40X... thanks a lot..
roshanbernard is offline   Reply With Quote
Old 06-26-2013, 08:11 AM   #4
ajthomas
Senior Member
 
Location: Utah

Join Date: Mar 2010
Posts: 162
Default

You might consider doing one run on a MiSeq or something and mixing that data with your Ion Torrent data to correct the indels. You might also consider using 454 instead of Ion Torrent since the longer reads will aid in assembly. 1/8 of a plate would give you the coverage you're looking for.
ajthomas is offline   Reply With Quote
Old 06-26-2013, 11:19 AM   #5
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

If you are considering other platforms, for about half the price (based on looking at one core lab's prices) of the 454 data you could run only Pacific Biosciences and almost certainly get a superior assembly.

How many strains are you sequencing & what are you estimating for the full cost per strain (library prep, sequencing) on Ion Torrent? On PacBio, your genome should be <$700 each.
krobison is offline   Reply With Quote
Old 06-26-2013, 08:07 PM   #6
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

My boss is interested in ion torrent.. because we have got that machine in our institute.. however yesterday we spoke to applied biosciances, they said they are gonna use 318chips with 100X coverage... dont know if i can get the proper aqssembly. i use geneious for the assembly....
roshanbernard is offline   Reply With Quote
Old 07-01-2013, 04:19 AM   #7
jonathanjacobs
Member
 
Location: Rockville, MD

Join Date: Apr 2011
Posts: 23
Default

For what it's worth - higher coverage will NOT not lead to better de novo assemblies. Once you hit about 40-50x , higher coverage may actually produce worse assemblies. Using an Ion318 for a 2MB genome is IMHO a waste of a chip and funding. You would be much better off running a 316 or even a 314 (314's in our lab routinely return 50-60mb of data, more than enough for a 2mb genome) and then using the money you save to outsource a PacBio or Illumina MiSeq run and then do a hybrid assembly.

That's my 2
jonathanjacobs is offline   Reply With Quote
Old 07-01-2013, 05:24 PM   #8
roshanbernard
Member
 
Location: South Korea

Join Date: Feb 2011
Posts: 31
Default

Quote:
Originally Posted by jonathanjacobs View Post
For what it's worth - higher coverage will NOT not lead to better de novo assemblies. Once you hit about 40-50x , higher coverage may actually produce worse assemblies. Using an Ion318 for a 2MB genome is IMHO a waste of a chip and funding. You would be much better off running a 316 or even a 314 (314's in our lab routinely return 50-60mb of data, more than enough for a 2mb genome) and then using the money you save to outsource a PacBio or Illumina MiSeq run and then do a hybrid assembly.

That's my 2
thanks a lot jonathan. Our preference was to save money. we are not interested in gap filling and stuff. we were looking for some specific genes. we have 84 bacterial samples for sequencing. Ur info is helpful. thanks a lot.
roshanbernard 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 06:31 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO