We have released Auto PeakTrace 5.63. This is a small bug fix update to correct an issue with outputting both .phd.1 and .seq files at the same time. It will be automatically updated if you are running Auto PeakTrace online, but if you wish to install Auto PeakTrace manually then it can be downloaded from the Nucleics Downloads page.
Chinese Version of Auto PeakTrace Released
We have released a Chinese language version of Auto PeakTrace. This version is exactly the same as the English language version, but it has been adapted to Chinese. To obtain a copy please contact our Chinese agent Shanghai BOQ Biotech Ltd.
我们已经发布了中文版的 Auto PeakTrace。 该版本与英文版的PeakTrace功能一致，并对界面进行了汉化。如果需要中文版的PeakTrace，请和我们在中国的代理商上海毕欧桥生物科技有限公司（Shanghai BOQ Biotech Ltd.）联系。
PeakTrace 5.62 Linux x86 Released
We have finally updated the Linux Release of PeakTrace to version 5.62 (yes it has been a long time). Due to changes in the CodeMeter runtime support we have had to create two version of PeakTrace – one for REHL 5 (CentOS 5.11+) and another for REHL 6 (CentOS 6.6+).
The two packages are available on Nucleics Download page. It is highly recommend that all linux users upgrade to this version.
Here is the complete change list for this version.
- Improved basecalling of rapid run traces.
- Improved basecalling of mixed template traces.
- Improved handling of failed traces.
- Updated system requirements.
- Bug fix for basecall alignment for short skipped traces when using trace trim.
- New Feature. Failed traces are now not charged. The exceptions are:
- Traces below the good base improvement threshold where the good base improvement threshold is set to a value higher than -10.
- Traces that can’t be output because the output folder is unwritable.
- New Feature. Faster basecalling and processing. PeakTrace processing is approximately 120% faster than 5.51.
- New Feature. Support added for the following run conditions:
- ABI 3730 Low Voltage POP7 BigDye 3.1
- ABI Limits are only updated for successful traces
- Improved basecalling and trace trimming.
- New Feature. A nolog option to suppress output of the PeakTrace logfile (command line only).
- Improved fuse basecalling option.
- Improved basecalling through large dye peaks.
- A short trace is now considered to be a trace with fewer than 500 bases.
- Improved support for ET terminator traces.
- Improved support for ABI3500 BigDye 1.1 traces.
- New error code 36 added – Input and output paths are the same.
- New error code 38 added – Skipped short trace.
- Good quality threshold and N base threshold now have maximum values of 99.
- The usual bug fixes and tweaks.
Auto PeakTrace 5.61 Released
We have released a minor update for Auto PeakTrace that fixes a problem with skip short traces when trace trimming is enabled. It is recommend that anyone running Auto PeakTrace 5.61 upgrade to this version. You will also need to upgrade to the latest version of the CodeMeter runtime (5.20b) to use this version.
Auto PeakTrace 5.61 is available on Nucleics downloads page and will be added to the automatic update shortly.
PeakTrace 5.60 Released
PeakTrace 5.60 has been released for Windows (other versions will follow in the next few days). This is a major release and we recommend everyone upgrade to this version. The two biggest changes are the Auto PeakTrace is over twice as fast as before and failed traces are now not counted towards your usage except in a few limited cases. This change effectively means that a price cut of between 20% to 50% depending on the number of traces that were not being improved (this varies from site to site) making PeakTrace an even better deal. If you were previously sorting traces by hand to avoid processing traces likely to not be improved by PeakTrace then you can avoid doing this and just process all traces without worrying about wasting your units. You can download the new version from our downloads page.
The complete list of changes in Auto PeakTrace 5.60 are:
- New Feature. Failed traces are now not charged. The exceptions are:
- Traces below the good base improvement threshold where the good base improvement threshold is set to a value higher than -10. If using the default value of -20 then you will not be charged.
- TraceTuner basecalled traces that fail TraceTuner basecalling.
- Traces that can’t be output because the output folder is unwritable.
- New Feature. Faster basecalling and processing. PeakTrace processing is approximately 120% faster than 5.51.
- New Feature. Support added for the following run conditions:
- ABI 3730 Low Voltage POP7 BigDye 3.1
- ABI Limits are only updated for successful traces.
- Improved basecalling and trace trimming.
- The usual bug fixes and enhancements.
CodeMeter runtime server has stopped working on Linux
A few of our customers are using the Linux version of PeakTrace and today I received a report from one of them that the codemeter runtime server has stopped working in Linux. I check my linux development box and it had stopped working there too. I then check on wibu’s site and I noticed that a new Codemeter runtime had been released around a month ago so I decide to checked to see if this fixed the problem and it did. I will be contacting wibu to find out why this happened and why no warning was given, but in the meantime updating to the new runtime fixes the problem.
This is the step-by-step process for updating the run time.
- Download the latest CodeMeter (6.40) and AxProtector (9.20) runtime for x64 Linux from here.
- Remove the current runtimes from your system using rpm.
- Find the right package names using:
- rpm -qa | grep codemeter
- rpm -qa | grep axprotector
- Remove the old packages using rpm -e <packagename>
- Find the right package names using:
- Install the new packages using rpm -ivh <packagename>
Check that the CodeMeter server is running (it should be now) and if it is you are good to go.
Auto PeakTrace & Auto PeakTrace RP 5.51 Update Released
We have released a small update for both Auto PeakTrace and Auto PeakTrace RP (5.51). This version just fixes a small bug with the use of a particular option set. We have also released new automatic updates for both these versions so if you are running an older version of these programs then you should be prompted to install the update at some point over the next week or so.
Auto PeakTrace 5.50 Released
A major update to Auto PeakTrace has been released. There will be updates released shortly for Auto PeakTrace RP and the Linux version of PeakTrace.
This update can be obtained from our downloads page. Please contact us for access to the downloads page if you do not have the password.
The complete list of changes are
- New Feature. A nolog option to suppress output of the PeakTrace logfile (comand line only).
- Improved fuse basecalling option.
- Improved basecalling through large dye peaks.
- Default options changed to improve basic usage
- .seq file output: abi
- required good base improvement: -20
- q average trim: Q12 average in 20 base window
- n base threshold: 5
- skip short traces: yes
- A short trace is now considered to be a trace with fewer than 500 bases.
- Improved support for ET terminator traces.
- Improved support for ABI3500 BigDye 1.1 traces.
- New error code 36 added – Input and output paths are the same.
- New error code 38 added – Skipped short trace.
- Good quality threshold and N base threshold now have maximum values of 99.
- The usual bug fixes and tweaks.
Publications mentioning the use of PeakTrace
I thought I would start posting papers that have mention that they have used PeakTrace. Here is the first of these posts — Phylogenetic Relationships of Muehlenbeckia, Fallopia, and Reynoutria (Polygonaceae) Investigated with Chloroplast and Nuclear Sequence Data published in International Journal of Plant Sciences, Vol. 172, No. 8. (October 2011), pp. 1053-1066. The authors of this paper claimed they were able to get 300 extra bases out of their reads using PeakTrace.
Changes to PeakTrace Online
PeakTrace Online (the free version of PeakTrace) has always used a very basic group of settings. One area that can cause it problems are traces with weak signal at the end of the trace. This is because PeakTrace Online was using any of the trace trim settings. While it should not really matter, some people get worried when seeing a large number of low quality base calls at the end of the trace. Personally I would rather have a low quality call rather than no call at all, but many people prefer these low quality regions removed.
To avoid this I have changed the online settings so that PeakTrace now uses the window quality score trimming options. PeakTrace Online will now trim any region where the average quality score in a 20 base window drops below 12 (i.e. -wq 12 20).