Ion Torrent PGM multiplexing

eosin · 03-27-2012, 08:14 PM

We're assessing the capabilities and cost-effectiveness of the Ion PGM so your answers will really help us.

How many bacterial genomes (let's say an average size of 4.6 MB like those found in e. coli) can be multiplexed in the Ion Torrent PGM 316 or 318 chip? Thanks!

low99 · 03-28-2012, 01:31 AM

It really depends on the coverage depth that you need.
What coverage are you looking for?

low99 · 03-28-2012, 07:52 AM

Basically it will come down to three things: output of your instrument, size of the genome and coverage required (what depth of sequencing do you need?)

314 chip highest output ~20Mb (20Mb/4.6Mb=4.3) so you could do one 4.6Mb genome at 4x coverage.

316 chip 200Mb (200Mb/4.6Mb=43) One genome at 43x coverage or 2 genomes at 21x coverage...

Typically if multiplexing is a priority, you should go for the instrument for the highest data output. The Illumina MiSeq has the highest at the moment with ~2Gb data output
(2Gb/4.6Mb=434)

1 genome sequenced 434 times OR
2 genomes @ 217x coverage OR
3 genomes @ 144x coverage OR
......10 genomes @ 43x coverage.....OR 20 genomes @ 21x coverage....etc...

So it's up to the desired depth of sequencing or coverage. The more you multiplex, the cheaper the sequencing cost per sample.

dukzilla · 03-28-2012, 11:51 AM

There is of course the 318 chip which will put out ~1Gb.

Thus with the 318 you can get (1000Mb/4.6Mb = 217) 217x coverage of one 4.6Mb genome and so on. But I guess the 318 chip is more expensive than the 316.

Do note that low99 is correct, the MiSeq has the highest coverage as the PGM is maxed out at 1GB (318 chip). I don't think Ion Torrent plans further chips development on the PGM.

For higher throughput using Ion Torrent technology, you'll need to upgrade/purchase the Proton.

Genomemirabilis · 03-29-2012, 10:50 AM

Actually, it would be ~2Gb with 318 with 200bp protocol.

eosin · 03-29-2012, 05:57 PM

Thank you guys! I understood everything much better now.

eosin · 03-29-2012, 05:59 PM

Actually we're planning to buy a MiSeq, PGM, and Proton. But I haven't got as much information about Proton as that of MiSeq and PGM.

dukzilla · 03-29-2012, 06:00 PM

Oh. I thought the 318 with the 200bp protocol was at 1GB output:
http://www.invitrogen.com/site/us/en...fications.html

Also on the Ion Community (RecognitION), the current highest run on the 318 is ~1GB:
http://lifetech-it.hosted.jivesoftwa...un_recognition

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03-27-2012, 08:14 PM	#1
eosin Junior Member Location: Philippines Join Date: Mar 2012 Posts: 7	Ion Torrent PGM multiplexing We're assessing the capabilities and cost-effectiveness of the Ion PGM so your answers will really help us. How many bacterial genomes (let's say an average size of 4.6 MB like those found in e. coli) can be multiplexed in the Ion Torrent PGM 316 or 318 chip? Thanks!

03-28-2012, 01:31 AM	#2
low99 Member Location: NYC Join Date: Feb 2012 Posts: 10	It really depends on the coverage depth that you need. What coverage are you looking for?

03-28-2012, 07:52 AM	#3
low99 Member Location: NYC Join Date: Feb 2012 Posts: 10	Basically it will come down to three things: output of your instrument, size of the genome and coverage required (what depth of sequencing do you need?) 314 chip highest output ~20Mb (20Mb/4.6Mb=4.3) so you could do one 4.6Mb genome at 4x coverage. 316 chip 200Mb (200Mb/4.6Mb=43) One genome at 43x coverage or 2 genomes at 21x coverage... Typically if multiplexing is a priority, you should go for the instrument for the highest data output. The Illumina MiSeq has the highest at the moment with ~2Gb data output (2Gb/4.6Mb=434) 1 genome sequenced 434 times OR 2 genomes @ 217x coverage OR 3 genomes @ 144x coverage OR ......10 genomes @ 43x coverage.....OR 20 genomes @ 21x coverage....etc... So it's up to the desired depth of sequencing or coverage. The more you multiplex, the cheaper the sequencing cost per sample.

03-28-2012, 11:51 AM	#4
dukzilla Junior Member Location: San Francisco Join Date: Dec 2010 Posts: 5	There is of course the 318 chip which will put out ~1Gb. Thus with the 318 you can get (1000Mb/4.6Mb = 217) 217x coverage of one 4.6Mb genome and so on. But I guess the 318 chip is more expensive than the 316. Do note that low99 is correct, the MiSeq has the highest coverage as the PGM is maxed out at 1GB (318 chip). I don't think Ion Torrent plans further chips development on the PGM. For higher throughput using Ion Torrent technology, you'll need to upgrade/purchase the Proton.

03-29-2012, 10:50 AM	#5
Genomemirabilis Junior Member Location: Brazil Join Date: Mar 2012 Posts: 5	Actually, it would be ~2Gb with 318 with 200bp protocol.

03-29-2012, 05:57 PM	#6
eosin Junior Member Location: Philippines Join Date: Mar 2012 Posts: 7	Thank you guys! I understood everything much better now.

03-29-2012, 05:59 PM	#7
eosin Junior Member Location: Philippines Join Date: Mar 2012 Posts: 7	Actually we're planning to buy a MiSeq, PGM, and Proton. But I haven't got as much information about Proton as that of MiSeq and PGM.

03-29-2012, 06:00 PM	#8
dukzilla Junior Member Location: San Francisco Join Date: Dec 2010 Posts: 5	Oh. I thought the 318 with the 200bp protocol was at 1GB output: http://www.invitrogen.com/site/us/en...fications.html Also on the Ion Community (RecognitION), the current highest run on the 318 is ~1GB: http://lifetech-it.hosted.jivesoftwa...un_recognition