Sequencing machines and electropherograms

[robekubica]

Hi everybody,

I've heard lately that new sequencing machines are not gonna add electropherogram information within the results given by them, only confidence values and text. Is that true?
At this case, is Sequencher software getting outdated?


I'm new at this genomic world, so I'd appreciate any comment or tip.

Thanks

[kmcarr]

Hi everybody,

I've heard lately that new sequencing machines are not gonna add electropherogram information within the results given by them, only confidence values and text. Is that true?

Next Generation Sequencing platforms (Roche/454, Illumina, SOLiD, etc) work in an entirely different way from earlier, Sanger based instruments. No electorpherograms exist on these platforms.

At this case, is Sequencher software getting outdated?

It will only become outdated if the developers choose to let it. A quick look at their website suggests that they are changing with the the technology.

Software is not the only thing that needs to change to accomodate the new technology. Researchers too need to change the way they design experiments which use DNA sequencing and the way in which they analyze the data.

[robekubica]

First of all, thanks Kmcarr.

But now, I have another pair of questions about electropherograms and software:

1) Is worst or just less efficient to work with electropherograms? What's the main reason to work without them?
2) Is Staden package (Gap4) able to do the same than Sequencher? I mean:
2.1) Assembly (map) to a reference sequence.
2.2) Edit the consensus secuence seeing the electropherogram at the same time.


Thanks again

PS: I'm watching the Sequencher website.

[pmiguel]

[/QUOTE]

First of all, thanks Kmcarr.

But now, I have another pair of questions about electropherograms and software:

1) Is worst or just less efficient to work with electropherograms? What's the main reason to work without them?

SEQanswers is primarily a "next generation" sequencing forum. Electropherograms are, by definition, a characteristic of first generation or "Sanger" sequencers.

That is, to collect massively parallel data sets, all second generation sequencers skip electrophoresis of the end-point sequencing reactions. Instead they all "watch" the polymerization of thousands or millions of product strands -- collecting information as each event (usually base incorporation) occurs.

The amounts of sequence collected by 1st vs 2nd generation sequencer is starkly different. The most popular 1st generation sequencer, the ABI 3730XL would have to be run non-stop for more than one year to equal the sequence output of a single Roche GS-FLX run. One 3730XL would have to be run for nearly two thousand years to equal the sequence output of a single Illumina HiSeq2000 run. (Although, to be fair, a HiSeq2000 2x100 PE run would take more than a week to complete.)


--
Phillip