Illumina produced Read Length

[Arupsss]

I am comparing BowTie vs BWA for various read lengths. Now, before one year ago Illumina produced read lengths are typically 36, 75 or 100 bps which they have increased now a days. Can anybody provide me information about, what is the typical read lengths that Illumina is producing now a days.

[GenoMax]

Since you asked for typical lengths ....

On HiSeq 2000 - 100 bp paired end runs are common (though people do run longer lengths).

With the v2. upgrade MiSeq is now capable of running 250 bp paired end runs as reported in this thread (http://seqanswers.com/forums/showthread.php?t=22561) yesterday.

Correction: MiSeq's (v.1.0/"original" release) that are currently in most labs are capable of doing up to 2 x 150 bp runs.

[adaptivegenome]

i would recommend 250 and 400bp and i would compare performance using SE and PE

[pmiguel]

Since you asked for typical lengths ....

On HiSeq 2000 - 100 bp paired end runs are common (though people do run longer lengths).

With the v2. upgrade MiSeq is now capable of running 250 bp paired end runs as reported in this thread (http://seqanswers.com/forums/showthread.php?t=22561) yesterday.

Do you know this? That is, do you have a MiSeq that is doing 250 nt. reads?

I think what you mean is that "at least one MiSeq is capable of running 250 nt paired end runs".

Let's not buy into the Illumina marketing hype because of a report from one person of an instrument upgrade. I don't think more than a few percent of the MiSeqs in the field are currently capable of this.

--
Phillip

[GenoMax]

To answer your question "no we do not have a MiSeq that is capable of 250 nt runs .. yet". Technically you are correct in saying that there are perhaps only a handful of MiSeq's in the wild that are capable of doing 2 x 250 bp runs *at this time*.

We are scheduled to get the upgrade next month. Do you have any information that indicates that this upgrade is not going to pan out?

Since the thread I had linked to was started by the owner of this site I do not see a reason not to believe him when he stated that they were in the middle of a 2 x 250 bp run on their MiSeq. (Eco can you send an update on what happened to the run you had posted in the MiSeq thread you had started)

Note: I have edited my original response to reflect the "typical" run values for an "original" (v.1.0) MiSeq.

Do you know this? That is, do you have a MiSeq that is doing 250 nt. reads?

I think what you mean is that "at least one MiSeq is capable of running 250 nt paired end runs".

Let's not buy into the Illumina marketing hype because of a report from one person of an instrument upgrade. I don't think more than a few percent of the MiSeqs in the field are currently capable of this.

--
Phillip

[adaptivegenome]

The intent here was to determine what read length were useful for evaluating two mappers on their ability to map Illumina reads. Many short reader mappers will behave differently once you exceed read lengths of 150bp. And since the future almost certainly involves read lengths of 250 and more, arupsss should certainly consider longer read length when doing his benchmarks.

[pmiguel]

To answer your question "no we do not have a MiSeq that is capable of 250 nt runs .. yet". Technically you are correct in saying that there are perhaps only a handful of MiSeq's in the wild that are capable of doing 2 x 250 bp runs *at this time*.

We are scheduled to get the upgrade next month. Do you have any information that indicates that this upgrade is not going to pan out?

Since the thread I had linked to was started by the owner of this site I do not see a reason not to believe him when he stated that they were in the middle of a 2 x 250 bp run on their MiSeq. (Eco can you send an update on what happened to the run you had posted in the MiSeq thread you had started)

Note: I have edited my original response to reflect the "typical" run values for an "original" (v.1.0) MiSeq.

No, that isn't what I mean at all. I do not doubt in the least that ECO has had his instrument upgraded. Nor that Illumina is capable of producing 250 nt reads on MiSeqs. I am just disgruntled with the usual Illumina marketing hype and don't like to see unwarranted re-trumpeting here in a neutral site.

Nor do I mean to blame you for this. In the context of you as a MiSeq owner, speaking to other MiSeq owners, or others with a (fairly) deep understanding of the current MiSeq upgrade path, I have zero problems with what you posted. But this forum is read by many who will only have heard what Illumina marketing is putting out there. So they may get the wrong idea -- that we are confirming the general availability of 250 nt reads on MiSeqs.

Furthermore, my understanding is that 250 nt reads do not require any hardware upgrade, just the MCS 2.0 software upgrade. You won't get the substantial (more than double) increase in number of reads until the hardware upgrade gets done. But being able to do 250 nt reads is a big deal. Yet, near as I can tell, that software is not yet generally available for download. See, for example, here.

--
Phillip