Has anyone used this DNA sequencing product before? - (Mar/06/2006 )

I am wondering if anyone has used this DNA sequencing website LongTrace yet? They claim that it can increase your traces read lengths by 30% - I find this hard to believe, but the trace picture looks pretty impressive! I want to try it out, but I noticed that you need to give them your email address - I am worried about spam so I would like to know if anyone else has used it before trying it myself . I guess on a positive side they do give you a 100 traces worth for free

I am glad to see that somebody here has found our new LongTrace sequencing service

RWhity yes the service will improve your traces by up to 30% - the record is a 122% increase, but this was due to our software overcoming a bug in ABI's KB base caller! Overall we find most people's read lengths are improved by around 15-20%. The reason we are able to get this improvement is because we are reprocessing the raw data in the ABI trace file before having KB re-base call the trace. This way you get an normal ABI KB base called trace, but only better. As for why we can do this, basically our software guys are better than ABI's

As for spamming you no we won't. We have a very strict privacy policy which you can read on our web site. We have been around since 1999, but we have only recently started selling our products to smaller users (all our previous customers are the large genome sequencing centres). If you are still worried about this then just use a throwaway email account for the registration.

If anyone has any questions about the LongTrace DNA sequencing service then either PM me or post your questions here and I will do my best to answer them.

Daniel

Thanks Daniel for your reply. I will give LongTrace a try and let everyone here know how it goes.

PS. I like the reviews of DNA sequencing facilities you have on your website, they have proved very useful

Great. I look forward to hearing what you think - all good I hope

Thanks for the comments about the reviews we put up. Basically we got sick of writing back to people telling them that we don't do standard DNA sequencing (I think the cause of this is our DMOZ listing is incorrect). Anyway if anyone else is interested in seeing these reviews the link is below (shamless plug ).

Reviews of DNA sequencing facilities

Daniel

Review of LongTrace

OK as promised here is my review of Longtrace - sorry it is a bit short.

Registering

This was pretty straight forward. I just followed the instructions. I used a new email account and so far no spam (good).

Processing traces

I uploaded 20 traces. Some were good traces and some were failed reactions or mixed template. 15 of the traces were processed with an average read length increase of 13.45% or 102 bases.

Only the traces that were processed successfully (15) were deducted from my balance (good).

Longtrace sends you an email summary of the results which is quite nice as you have a permeant record of what has been processed.

The traces looked much better. I have attached a couple of picture of a trace before and after Longtrace to show what they look like.

Issues

The visual help manual is missing. This is not too much of a problem as the website is fairly obvious how to use, but it might be problem for some people.

The software only appears to work with 3730 traces. I tried processing an old 3700 traces file I had, but it was not successful. It would be nice if the longtrace was able to process 3700 traces.

Conclusion

Overall the LongTrace looks like a very useful service provided that you have a 3730 sequencer. I like that you can test it on your own traces for free. I will certainly be using it again in the future.

RWity

Thanks for you review - it is always nice to see people happy with our products - the trace file look good too

You raised a couple of points which I should answer. Yes the LongTrace service currently only works with ABI 3730 traces. We are working on supporting 3100 and 3130 traces, however, the problem with 3700 traces is ABI never released a version of KB that works with the 3700. As the base calling in LongTrace is done by KB we can't support 3700 traces as the system is currently designed. We have thought about using phred for the base calling, but we would need a large data set for training. If anyone here has 20,000+ 3700 traces of known sequence and would mind sharing them with us then either PM me or email me at Nucleics.

The visual help manual hasn't been finished yet, hopefully it will be up by the end of the week. This is my job, but I have been so busy that I haven't had time to finish it off.

Daniel

Just a quick follow up on this thread if anyone is interested. I have been using longtrace quite a bit of late and it has been a real help. I have been primer walking through a pretty big gene and I was able to start spacing out my primers an extra 150 base further apart than I was using previously. It has saved me quite a bit of time and money

I might soon actually have to start paying for the service as I have nearly used up all of my free processings

Just a quick follow up on this thread if anyone is interested. I have been using longtrace quite a bit of late and it has been a real help. I have been primer walking through a pretty big gene and I was able to start spacing out my primers an extra 150 base further apart than I was using previously. It has saved me quite a bit of time and money

I might soon actually have to start paying for the service as I have nearly used up all of my free processings

Churb - all you need to do if upload your ABI trace file to the LongTrace server and all the processing happens automatically and you end up with a longer read. I would encourage you to just try it on some of your traces - it is free and as it works on a copy of your trace it can't hurt them. If you have any other questions either PM me or post here.

RWhity- I am glad to hear that you have been finding LongTrace useful - maybe we should reduce the number of free samples we give people

I just thought I would drag up this old topic to let everyone know that we have added a free version of LongTrace online that you don't need to register for to use. This version is limited to only process 10 traces a day, but it is free

The other thing I should mention is that LongTrace can now process ABI 3100 and 3700 traces as well as 3730 traces. So if you have one of these machines you might want to take another look at it.

The free version can be accessed here:

http://www.nucleics.com/longtrace-sequencing/

Cheers

Daniel