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We have added a separate forum just for discussion of the LongTrace:Box system. If you have any questions about the system please post them there.
Daniel Tillett
Nucleics SupportThe bad news is you can’t just buy the LongTrace software as LongTrace is just too complex to set up and computational expensive to be suitable as a user installable software.
The good news is we have just launched a new hardware/software LongTrace system (called imaginatively LongTrace:Box). This is basically the LongTrace software set up on a small computer (an Apple Mac mini running Windows XP) which you can just plug into your network and use at you facility without having to upload your traces to our ftp server. This only limitation with LongTrace:Box is you need to be processing at least 2000 traces a month for it to be cheaper than using the ftp based system.
Daniel Tillett
Nucleics SupportYou really need to look at your sequencing protocol. Our experience is the DNA template seems to be the critical component.
The simplest thing to do is run your traces through our free QualTrace server (https://www.nucleics.com/qualtrace-dna-sequencing-demo/) and see what the it says is the problem with your traces.
If the problem is weak ends then there are two things to try that will help. 1. Try a template concentration range, both higher and lower (10 fold) than what you are currently using, and 2. Try increasing the annealing and extension thermocycling times (15 s and 5 minutes).
Cheers
Daniel Tillett
Nucleics SupportYes there is a linux version, however, there is no linux version of Auto QualTrace so you have to use the command line version (this shouldn’t be a problem for any linux user).
No the source code is not available, but I guess if you were to offer us enough money then we might change our minds 🙂
Daniel Tillett
Nucleics SupportWell after taking longer than we hoped the full LongTrace system is back online. You can access it here at [www.nucleics.com]
The bad news is you will need to register even if you had been previously registered. The good news is you will get another 100 free trace processings.
Daniel Tillett
Nucleics SupportNot a problem rgrant 🙂
There are quite a few that are quite low cost facilities if you want to send ready-to-run samples. Probably the cheapest is UCLA Core Facility at $150 for a 96 well tray which is only a $1.56 a trace. Have a look through the reviews we have done (www.nucleics.com/DNA_sequencing_support/sequencing-service-reviews.html) if you haven’t already.
Cheers
Daniel Tillett
Nucleics SupportThere are two ways of ordering. The simplest is to use our secure online ordering system. There is a link to this from the dLUTE SEQ information page. You will need an credit card to use this system. The alternative is to email our support staff with your order. You will need to use this approach if you want to use a purchase order.
Daniel Tillett
Nucleics SupportThis really depends on what services you want and how many samples that you want to process at a time. Some sequencing facilities are very cheap if you send in a minimum of 96 samples in a tray, while others are much better for only a few samples.
The other major area that can make quite a difference in price is if you want to do your own reactions or not. can you provide more information of what you want?
Daniel Tillett
Nucleics SupportI have to say I prefer Macs too. I will see what we can do, but don’t expect anything in the next few months 🙂
Daniel Tillett
Nucleics SupportIt should be back online in around a weeks time. It will be quite different to the previous system. If you are really in a hurry please email or PM me and I will arrange for you to use the alpha version.
Daniel Tillett
Nucleics SupportI am glad to hear this. If anyone else tries LongTrace with ABI 3730 or 3100 traces we would really like to hear from you – either positive or negative.
Daniel Tillett
Nucleics SupportUsually you will get your traces back in under a minute – it depends a bit on how many traces you have uploaded and how many other people are using the server.
Reprocessing traces from incomplete BAC assemblies works really well. We did a study earlier in the year looking at exactly this. Just by re-processing we were able to turn BACs that couldn’t be assembled into single contigs. If you want to try LongTrace on a BACs worth of traces send me a PM or email me and I will arrange for a large scale trial.
Finally, don’t throw out your ab1 traces! The reason that they are bigger than the scfs is they contain the raw trace data. It is by reprocessing the raw data that LongTrace can get longer reads.
Cheers
Daniel Tillett
Nucleics SupportNo unfortunately not. We want to make a mac version (I personally use a mac), the problem is a lack of resources. It is on our to-do-list.
Daniel Tillett
Nucleics SupportNone at all. This is in fact the best way to make use of LongTrace – change your set up to make best of the increase in read length.
If you haven’t already tried the free service then give it try. The only thing to watch for is make sure that the traces you use are long enough for LongTrace to actually make a difference – there is no point processing 500bp PCR fragments because the trace signal ends before the normal resolution of the sequencer is reached (ie the signal is already as good as it could be before longtrace processing).
Daniel Tillett
Nucleics SupportHi Paola
I don’t know of any sequencing facilities in South America, so I would suggest using any of the facilities in the USA that are shown in red on the main sequencing facility review pages. These are customers of ours that are using LongTrace or PeakTrace and that I know generate good quality data – speed is not much help if what you get back is not good quality 🙂
Daniel Tillett
Nucleics Support
