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• File released: /trace-utils/0.1.0-pre3/trace_utils-0.1.0-pre3.tar.bz2

  posted 1886 days ago

• Code committed

  lihengsci committed patchset 79 of module trace_utils to the Trace Utilities CVS repository, changing 25 files

  posted by lihengsci 1886 days ago

• trace-utils 0.1.0-pre3 file released: trace_utils-0.1.0-pre3.tar.bz2

  posted 1886 days ago

• File released: /trace-utils/0.1.0-pre1/trace_utils-0.1.0-pre1.tar.bz2

  posted 1905 days ago

• File released: /trace-utils/0.1.0-pre2/trace_utils-0.1.0-pre2.tar.bz2

  posted 1905 days ago

• Code committed

  lihengsci committed patchset 78 of module trace_utils to the Trace Utilities CVS repository, changing 28 files

  posted by lihengsci 1905 days ago

• trace-utils 0.1.0-pre1 file released: trace_utils-0.1.0-pre1.tar.bz2

  See ChangLog in the package

  posted 1905 days ago

• trace-utils 0.1.0-pre2 file released: trace_utils-0.1.0-pre2.tar.bz2

  Please ChangeLog in the release package

  posted 1905 days ago

• Code committed

  lihengsci committed patchset 77 of module trace_utils to the Trace Utilities CVS repository, changing 1 files

  posted by lihengsci 1924 days ago

• Alpha Release 0.1.0-pre1

  This is the first version of trace_utils, a utility for trace file processing. Trace_utils was initiated by HLA project. The original goal was to develop an software that was capable of automated base-calling and HLA typing. At first, I tried to modify phred source codes so as to make phred call heterozygote bases. It was achieved in March, but I also realized that single-trace base-calling could be in no way accurate enough for the original goal. I gave in at last. Then Xu Zhao and I invented a cluster-based algorithm to achieve more accurate base-calls. This project is still in active development maintained by Xu Zhao. The main branch of trace_utils project was actually started in late April, when I had successfully written a simplified implementation of trace subtraction method. It was amazing, and I believed that it would lead to an accurate method in heterozygote detection. Then I knew, in early June, that this idea was not brand-new at all. It has been successfuly implemented in traceDiff, a mutation dector in Staden Package. However, different from traceDiff, trace_utils utilizes some statistical methods and can accurately assign probability-based score to each base, like what phred has done. One month ago, I incorporated typing utilities into trace_utils and I for the first time can see a glimmer of hope to the original goal: an automated base-caller and HLA typing software, though I know there is still a long way to go. As the original trace_utils was just a core engine that is hard to use for end-users, several interfaces were devloped when I moved this project to soureforge.net. They included two graphical typing interfaces, one consed interface and one batch typing script. Unfortunately, the two graphical ones are not open source. You can of course write your own interface, but it is not easy at all.

  posted by lihengsci 1924 days ago