Autofinish and Consed Improvements --------------------------------------------------------------------- Autofinish Improvements * Reverses (universal primer reverse reads) are now suggested in order to close gaps and improve low quality regions in addition to flanking gaps. * Autofinish now evaluates itself--after you do the reads it suggests, you can run it and it will tell you how well the reads solved the problems they were supposed to solve. * Oligos are tagged (when you use -doExperiments). * doNotFinish tags can be used to tell autofinish to not try to finish particular regions. * There are many more flags, allowing you a great amount of control over autofinish. For example, if you wanted the first round of autofinish to not choose any custom oligo experiments, fine. If you wanted autofinish to only close gaps and not improve the error rate within contigs, fine. * The autofinish output is very detailed and verbose. Thus in addition there are 3 summary lists of experiments to do (one file for forward universal primer experiments, one file for reverse universal primer experiments, and one file for custom oligo walks.) These summary files are easily imported into Excel. You can use the last one to email order oligos. --------------------------------------------------------------------- Consed: * Consed already had the ability to tear a contig into 2 and join 2 contigs into one. Now it also has the ability to move a single read to a different location within an assembly. Now you have much better control in fixing a misassembly. * You used to be able to compare a contigs to one other contig. Now you can compare a contig to many other contigs. * For sites with LONG, LONG read names: you can now customize how much space consed saves for displaying read names. You can also customize the initial size of the important windows. * In the Traces Window, you can move left and right with the arrow keys. * In the Aligned Reads Window, you can instantly move to the beginning and/or end of a read. Similarly, you can move instantly to the beginning and/or end of the consensus. * The ABI base calls can be hidden, if you like, thus allowing you to see more traces at once. * All documentation windows can be searched and printed out. * In the past you could see all tags of a particular type for a particular contig. Now there is also a function to see all tags of a particular type in any contig. * You can now write all contigs to a file in FASTA format with a single click. * You can navigate to multiple locations while staying in the Aligned Reads Window--you don't have to switch windows with each location. * Navigate by single stranded regions and navigate by single subclone regions used to depend on the dim settings to decide whether it counted low quality regions or not. Now these functions do not depend on the dim settings. * For the primers that consed picks, consed will show you the alignment of the closest false match. This will help you in deciding if you want to raise consed.primersMaxMatchElsewhereScore * The template picking part of primer picking has been further improved: ------------------------------------------------- (template) ---> (primer) <----distance to end of template----> This 'distance to end of template' gives the longest read you could possibly make with this primer and this template. If this distance is too short, you can now reject the template. The consed resource to set is: consed.primersWhenChoosingATemplateMinPotentialReadLength: 500 * If you want to pick templates yourself, you can turn off consed's template picking. This is particularly useful if you haven't bothered to customize determineReadTypes.perl * If you are using an old version of phred or if you haven't installed it correctly (with all kinds of bad effects), consed will warn you. * Previously, consed reported the error rate for a contig. But some contigs have long tails of low quality bases and you would like to know the error rate for the contig without that long tail. Now you can do that: You can get the error rate for a specified region. * Programmers can now append RT tags to the ace file. (See FOR PROGRAMMERS AND FELLOW TRAVELLERS in README.txt) * Programmers can popup a trace by a command from a different program. --------------------------------------------------------------------- Note to Linux users: The 'scroll all traces' bug is fixed. Note to Solaris 2.7 users: Consed now works on this version of solaris.