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    <title>LongTrace Forum</title>
    <link>http://www.nucleics.com/forum/list/3.html</link>
    <description><![CDATA[Questions & discussion about the LongTrace DNA sequencing service]]></description>
    <language>EN</language>
    <pubDate>Thu, 20 Sep 2007 03:33:50 -0400</pubDate>
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    <category>LongTrace Forum</category>
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    <item>
      <title>Re: how does long-trace work?</title>
      <link>http://www.nucleics.com/forum/read/3/336/355.html#msg-355</link>
      <author>nucleics</author>
      <description><![CDATA[Hi Mira

If your trace is giving &quot;weak or failed&quot; traces at the end it means that the signal at the end of the trace is too low to be improved by LongTrace. I can't really tell you much more without seeing you trace, but if you open you trace in a trace viewing program like FinchTV you can have a look at the signal at the end of the trace. You need to look at the raw data as this is what LongTrace uses to do the basecalling. If the peak signal at the end of the trace is very weak (basically flat) then LongTrace is not able to do much to improve the basecall.

A trace file is just the ab1 file that contains the sequence data peaks. I don't really know why they are called trace files - I guess there is some sort of historical reason for it.

The free service has a limit of 10 files per day - it is really only for tiny users and people wanting to try LongTrace. If you want to process more files then this you need to register for LongTrace FTP. The link to regester is here

[url=https://www.nucleics.com/longtrace/user-app.php]LongTrace Registration[/url]

Finally, have you tried PeakTrace too? Sometimes it is able to improve traces that can't be improved by LongTrace. The link for the free PeakTrace version is here:

[url=http://www.nucleics.com/peaktrace-sequencing/]Free PeakTrace Basecaller[/url]

Cheers]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/336/355.html#msg-355</guid>
      <pubDate>Thu, 20 Sep 2007 03:33:50 -0400</pubDate>
    </item>
    <item>
      <title>Weak or failed trace</title>
      <link>http://www.nucleics.com/forum/read/3/336/352.html#msg-352</link>
      <author>mira</author>
      <description><![CDATA[Hi!
  I tried putting my sequences for the free LongTrace DNA sequencing service. My seq were in the correct ab1 format but i only got this reply 'Weak or failed trace'. Can you help me out? For your info, the sequences i put in is about 800 bp in length.
   Also can you explain a bit about the 10 trace limit per person? What does the term 'trace' refer to?
    I'm rather new at this and i'de like to understand more if its not too much trouble.

Thank you :)]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/336/352.html#msg-352</guid>
      <pubDate>Thu, 20 Sep 2007 02:40:43 -0400</pubDate>
    </item>
    <item>
      <title>Re: how does long-trace work?</title>
      <link>http://www.nucleics.com/forum/read/3/336/341.html#msg-341</link>
      <author>nucleics</author>
      <description><![CDATA[Hi Resnanti

How LongTrace works is a trade secret, but in general terms it does the same type of processing that ABI's software does only we are better at it than ABI. I know these seems strange as the guys at ABI are pretty smart. I suspect the ABI management doesn't think it is a priority to improve the processing of their own traces and hence the software people there don't work on it. 

In the end it doesn't really matter - what matters is does LongTrace improve your own traces and the best of finding that out is trying our free [url=http://www.nucleics.com/longtrace-sequencing/]LongTrace DNA sequencing service[/url]. Hopefully you will like what you see :)

You might also want to check out our new basecaller PeakTrace. This works much like LongTrace, but on a wider range of machines (it can even improve ABI 377 trace). You can also try it for free at the [url=http://www.nucleics.com/peaktrace-sequencing/]PeakTrace DNA sequencing basecaller[/url] page.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/336/341.html#msg-341</guid>
      <pubDate>Thu, 13 Sep 2007 21:21:55 -0400</pubDate>
    </item>
    <item>
      <title>how does long-trace work?</title>
      <link>http://www.nucleics.com/forum/read/3/336/336.html#msg-336</link>
      <author>resnanti</author>
      <description><![CDATA[i wonder how does long trace software work with ab1 file? thx]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/336/336.html#msg-336</guid>
      <pubDate>Tue, 04 Sep 2007 03:50:36 -0400</pubDate>
    </item>
    <item>
      <title>LongTrace FTP usage reporting update</title>
      <link>http://www.nucleics.com/forum/read/3/335/335.html#msg-335</link>
      <author>nucleics</author>
      <description><![CDATA[We have updates the usage reports to make it a little easier to understand how many traces you have processed and how many processing units remain. 

You can access your usage report by logging in to the main LongTrace page and entering your ftp user name and password in the login box.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/335/335.html#msg-335</guid>
      <pubDate>Mon, 03 Sep 2007 20:14:57 -0400</pubDate>
    </item>
    <item>
      <title>Re: LongTrace for 3700 released</title>
      <link>http://www.nucleics.com/forum/read/3/105/330.html#msg-330</link>
      <author>nucleics</author>
      <description><![CDATA[If you are interested in using LongTrace for the 3700 we suggest you check out our PeakTrace service as it performs much better on 3700 traces than LongTrace does.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/105/330.html#msg-330</guid>
      <pubDate>Mon, 20 Aug 2007 03:51:00 -0400</pubDate>
    </item>
    <item>
      <title>New Basecaller (PeakTrace) released</title>
      <link>http://www.nucleics.com/forum/read/3/326/326.html#msg-326</link>
      <author>nucleics</author>
      <description><![CDATA[We are happy to announce that we have finally released our new base caller, PeakTrace. This has been designed to work with traces from all ABI DNA sequencers, including even old sequencers like ABI 377 and ABI 3700. The quality is comparable or better than that offered by LongTrace so it worth a look.

You can find out more about PeakTrace by visiting the [URL=https://www.nucleics.com/peaktrace/]PeakTrace base caller[/URL] information page and you can try it at the [URL=http://www.nucleics.com/peaktrace-sequencing/]free PeakTrace basecaller[/URL] page.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/326/326.html#msg-326</guid>
      <pubDate>Wed, 08 Aug 2007 04:00:27 -0400</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/324.html#msg-324</link>
      <author>nucleics</author>
      <description><![CDATA[Hi Annoyed

I hope we are not insulting our customers by explaining why we don't just sell the software. The LongTrace software is computationally complex (it takes 7 to 15 seconds to process each trace). The mac mini is a surprisingly powerful computer (about equivalent to 3Ghz Pentium 4). To run LongTrace in a reasonable time it needs to be run on a fairly powerful computer - something that the mac mini offers in a small and silent package.

The major problem we face with just selling the software is that LongTrace uses the KB basecaller. LongTrace just process the traces and they are basecalled by ABI's KB basecaller. Because of the difficulty of setting this up correctly (we need to use KB in a non-standard way) it makes for a very brittle system, where unless we know exactly the state of the system it doesn't work. Given that the extra cost that the mac mini imposes on our customers is very low (~5% of the final price), and the fact that we are then faced with supporting only one system, we think that this makes sense for our customers - I would hope they value having a reliable, working and supportable system even if it comes at a slightly higher price.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/324.html#msg-324</guid>
      <pubDate>Sat, 04 Aug 2007 18:14:47 -0400</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/323.html#msg-323</link>
      <author>Annoyed</author>
      <description><![CDATA[While I appreciate the business model of keeping your software a &quot;service&quot;, please don't insult your users and potential customers by saying that the software is too 
&quot;computationally complex&quot; when it runs on a Mac Mini.  

If you don't want to sell the software, just say that it isn't part of your business model.

Best of luck.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/323.html#msg-323</guid>
      <pubDate>Sat, 04 Aug 2007 12:52:50 -0400</pubDate>
    </item>
    <item>
      <title>Re: Alpha ABI 310 support</title>
      <link>http://www.nucleics.com/forum/read/3/264/322.html#msg-322</link>
      <author>nucleics</author>
      <description><![CDATA[We have decided to move support for the 310 to our new software basecalling software PeakTrace. PeakTrace offers all the benefits of LongTrace, but with PeakTrace we are able to support a wider ranger of 310 run conditions. For more information please visit the PeakTrace information page.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/264/322.html#msg-322</guid>
      <pubDate>Thu, 02 Aug 2007 02:36:56 -0400</pubDate>
    </item>
    <item>
      <title>Alpha ABI 310 support</title>
      <link>http://www.nucleics.com/forum/read/3/264/264.html#msg-264</link>
      <author>nucleics</author>
      <description><![CDATA[We have developed support for the ABI 310 sequencer (quite a strange little sequencer - the traces are halfway between 3700 and 3100). This should be available in the next major LongTrace release which should be out in the next few weeks (fingers crossed), but if you can't wait then please contact us and we should be able to work something out (we are always looking for new beta testers).]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/264/264.html#msg-264</guid>
      <pubDate>Thu, 14 Jun 2007 21:36:59 -0400</pubDate>
    </item>
    <item>
      <title>Re: Why is the smallest size of the longtrace box is 5000?</title>
      <link>http://www.nucleics.com/forum/read/3/128/131.html#msg-131</link>
      <author>nucleics</author>
      <description><![CDATA[Hi Andrew

The reason is basically the cost of the software and hardware components of the LongTrace:Box system means that we wouldn't make any money if we charged less per month :-) You could just used the 5000 trace per month system and not worry that you are not using all the processings per month. This will have the effect of increasing the average cost per trace a little, but this should not be excessive - the price per trace would move from 10 cents to 16.6 cents a trace.

At 3000 traces a month you might find that it is better to use our online service instead - not only would it be cheaper (less than 12 cents a trace if you by a few month in advance), but it comes with the performance guarantee.

Cheers

Daniel]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/128/131.html#msg-131</guid>
      <pubDate>Thu, 19 Apr 2007 20:37:21 -0400</pubDate>
    </item>
    <item>
      <title>Why is the smallest size of the longtrace box is 5000?</title>
      <link>http://www.nucleics.com/forum/read/3/128/128.html#msg-128</link>
      <author>Andrew R</author>
      <description><![CDATA[Hi Nucleics

Can I ask why the smallest size of the longtrace box is 5000 traces a month? We would like to use longtrace but we only process 3000 traces a months. Do you sell a smaller version?

Thanks

Andrew]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/128/128.html#msg-128</guid>
      <pubDate>Tue, 17 Apr 2007 00:21:02 -0400</pubDate>
    </item>
    <item>
      <title>Re: LongTrace Upgrade March 2007</title>
      <link>http://www.nucleics.com/forum/read/3/108/118.html#msg-118</link>
      <author>nucleics</author>
      <description><![CDATA[Hi Rob

This is hard to answer as the 3700 traces don't have quality scores it you can't really measure the read length improvement. This release more improves the number of traces that are successfully processed rather than the amount that any one trace is improved. I should say that there is still quite a bit of work to do in regards supporting the 3700 so you should regard the current version as just a beginning.

Cheers]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/108/118.html#msg-118</guid>
      <pubDate>Thu, 05 Apr 2007 02:44:45 -0400</pubDate>
    </item>
    <item>
      <title>Re: LongTrace Upgrade March 2007</title>
      <link>http://www.nucleics.com/forum/read/3/108/117.html#msg-117</link>
      <author>Rob</author>
      <description><![CDATA[How much does this upgrade increase the read length of 3700 traces?]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/108/117.html#msg-117</guid>
      <pubDate>Tue, 03 Apr 2007 04:01:28 -0400</pubDate>
    </item>
    <item>
      <title>LongTrace Upgrade March 2007</title>
      <link>http://www.nucleics.com/forum/read/3/108/108.html#msg-108</link>
      <author>nucleics</author>
      <description><![CDATA[We have upgraded both the free and ftp version of LongTrace. This upgrade offers improved processing of a wider range of ABI 3730 and 3130 traces that provides more accurate base calling. It also increases the number of ABI 3700 traces that can be improved.

Daniel]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/108/108.html#msg-108</guid>
      <pubDate>Sun, 18 Mar 2007 18:50:45 -0400</pubDate>
    </item>
    <item>
      <title>Change to free LongTrace version</title>
      <link>http://www.nucleics.com/forum/read/3/107/107.html#msg-107</link>
      <author>nucleics</author>
      <description><![CDATA[We have modified the free version of LongTrace to output the LongTrace processed trace even when the increase in Q20 bases is less than 25 bases. This is so that you can see how LongTrace improves the trace even if your trace is not improved by 25 bases. We are working on a way of of doing this with the paid ftp based system under user control (ie allow our users to choose between process all traces or only those traces improvable by at least 25 bases).]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/107/107.html#msg-107</guid>
      <pubDate>Mon, 26 Feb 2007 19:16:56 -0500</pubDate>
    </item>
    <item>
      <title>LongTrace for 3700 released</title>
      <link>http://www.nucleics.com/forum/read/3/105/105.html#msg-105</link>
      <author>nucleics</author>
      <description><![CDATA[We have released a version of LongTrace that works with the ABI 3700 sequencer. This version offers improvements of up to 50% in read length. The traces after LongTrace processing look better than what you get from a 3730 so even I am quite impressed!]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/105/105.html#msg-105</guid>
      <pubDate>Sat, 27 Jan 2007 17:48:56 -0500</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/97.html#msg-97</link>
      <author>nucleics</author>
      <description><![CDATA[The cost of the standalone version is quite a bit cheaper than the online version at $500 for 5000 trace processing per month (10 cents a trace), $750 for 10,000 trace processing (7.5 cents), and $1250 for 25,000 traces processing a month (5 cents).


The downside of the LongTrace:Box system it doesn't come with any performance guarantees (ie you are charged per trace processed not per traces successfully processed) so you have to be processing a minimum number of traces per month for it to be cheaper (around 2000 successfully traces per month).]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/97.html#msg-97</guid>
      <pubDate>Sun, 03 Dec 2006 18:02:13 -0500</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/95.html#msg-95</link>
      <author>rwhitfield</author>
      <description><![CDATA[So how much does it cost?]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/95.html#msg-95</guid>
      <pubDate>Thu, 30 Nov 2006 20:27:04 -0500</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/91.html#msg-91</link>
      <author>nucleics</author>
      <description><![CDATA[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.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/91.html#msg-91</guid>
      <pubDate>Thu, 30 Nov 2006 01:09:55 -0500</pubDate>
    </item>
    <item>
      <title>Re: LongTrace and poor quality traces</title>
      <link>http://www.nucleics.com/forum/read/3/70/88.html#msg-88</link>
      <author>nucleics</author>
      <description><![CDATA[You 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 (http://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]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/70/88.html#msg-88</guid>
      <pubDate>Thu, 23 Nov 2006 19:06:11 -0500</pubDate>
    </item>
    <item>
      <title>Re: Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/87.html#msg-87</link>
      <author>nucleics</author>
      <description><![CDATA[The 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.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/87.html#msg-87</guid>
      <pubDate>Thu, 23 Nov 2006 18:48:26 -0500</pubDate>
    </item>
    <item>
      <title>Re: LongTrace and poor quality traces</title>
      <link>http://www.nucleics.com/forum/read/3/70/86.html#msg-86</link>
      <author>Muz</author>
      <description><![CDATA[So what should I do we traces that are not improved by LongTrace?]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/70/86.html#msg-86</guid>
      <pubDate>Wed, 22 Nov 2006 23:33:25 -0500</pubDate>
    </item>
    <item>
      <title>Can I buy the LongTrace software?</title>
      <link>http://www.nucleics.com/forum/read/3/85/85.html#msg-85</link>
      <author>Muz</author>
      <description><![CDATA[I don't want to use the ftp longtrace service. Can I just buy the longtrace software?]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/85/85.html#msg-85</guid>
      <pubDate>Wed, 22 Nov 2006 23:32:23 -0500</pubDate>
    </item>
    <item>
      <title>Re: When will the full version of longtrace be working?</title>
      <link>http://www.nucleics.com/forum/read/3/64/79.html#msg-79</link>
      <author>nucleics</author>
      <description><![CDATA[Well after taking longer than we hoped the full LongTrace system is back online. You can access it here at https://www.nucleics.com/longtrace

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.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/64/79.html#msg-79</guid>
      <pubDate>Mon, 06 Nov 2006 17:59:13 -0500</pubDate>
    </item>
    <item>
      <title>LongTrace and poor quality traces</title>
      <link>http://www.nucleics.com/forum/read/3/70/70.html#msg-70</link>
      <author>nucleics</author>
      <description><![CDATA[In general LongTrace does not work well with low quality traces. This is because LongTrace improves the signal present and for most low quality traces the signal is either not present (failed reactions, short reads) or can not be made sense of (mixed templates, noise traces).

The major exception to this limitation are traces that have very low resolution (blurry) and traces with high levels of signal crosstalk (large crosstalk look like mixed signal). These types of traces are often improved the most by longtrace. We have seen some traces showing these two problems that have had read length increase of over 150%.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/70/70.html#msg-70</guid>
      <pubDate>Tue, 10 Oct 2006 00:38:33 -0400</pubDate>
    </item>
    <item>
      <title>Re: When will the full version of longtrace be working?</title>
      <link>http://www.nucleics.com/forum/read/3/64/67.html#msg-67</link>
      <author>nucleics</author>
      <description><![CDATA[It 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.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/64/67.html#msg-67</guid>
      <pubDate>Wed, 04 Oct 2006 21:18:38 -0400</pubDate>
    </item>
    <item>
      <title>When will the full version of longtrace be working?</title>
      <link>http://www.nucleics.com/forum/read/3/64/64.html#msg-64</link>
      <author>maslunka</author>
      <description><![CDATA[When is the full version of LongTrace going to come back? I have a whole lot of traces I want to process.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/64/64.html#msg-64</guid>
      <pubDate>Wed, 04 Oct 2006 19:29:39 -0400</pubDate>
    </item>
    <item>
      <title>Re: Beta ABI 3130 and 3100 support</title>
      <link>http://www.nucleics.com/forum/read/3/50/59.html#msg-59</link>
      <author>nucleics</author>
      <description><![CDATA[I 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.]]></description>
      <category>LongTrace Forum</category>
      <guid isPermaLink="true">http://www.nucleics.com/forum/read/3/50/59.html#msg-59</guid>
      <pubDate>Tue, 03 Oct 2006 19:46:13 -0400</pubDate>
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