--------------------------------------------------------------------- Autofinish Improvements Autofinish has now proven itself--it is successfully in use in the Genome Center in Seattle. It is planned for installation at several other major sites around the country. It has allowed the same human finishers to handle many times as many BACs in the same length of time as without autofinish. Some BACs are completely finished by autofinish and submitted without any human decisions and without any editing. Here are the latest improvements to consed/autofinish: Tries to close gaps by walking and by resequencing with universal primer terminator reads. Gap closing experiments must extend into a gap a minimum number of bases to be considered (by default, this number is 30). Tries to flank gaps by calling universal primer reverses Clone ends (BAC, cosmid) are detected and autofinish will not extend into them Single subclone regions (region covered by a single template) are now covered. Templates are extensively checked: Vector is detected and thus the actual starting/ending locations of the insert is detected. This prevents walking into vector. All existing reads from this template are checked for consistency. This allows consed to find misassemblies, tracking errors, and mislabelled subclones, thus decreasing the failure rate due to picking the wrong template. This information also helps in determining the insert size. Must not have an unaligned high quality region (longer than a threshold) nor high quality discrepancies. This helps with locating templates that are misassembled or have deletions. Walking reads and whole clone reads are recognized (assuming you correctly modified the script determineReadTypes.perl) and thus do not indicate the start of a template. This also prevents walking into vector. You can turn off particular types of reactions (such as BAC sequencing reactions) if you don't want autofinish to call them. Previously, consed/autofinish had to be run from someone's monitor since it needed to open a display. Now when you run consed/autofinish, you can run this from a batch job (typically the same job that runs phrap) without it being on anyones terminal. Reports inconsistent fwd/rev read pairs. Contigs are excluded if their depth of coverage is out of line (likely contamination) ("Out of line" means more than twice the depth of coverage of the largest contig.) --------------------------------------------------------------------- Tear (split) a contig Tell Phrap Not To Overlap Reads Discrepant At This Location Has been made more powerful Add new reads If a read doesn't match well enough to go into the assembly, it is put into a contig by itself. (This is an option.) --------------------------------------------------------------------- Features of particular interest to people doing polymorphism detection and/or cDNA assemblies: Integration with POLYPHRED You can now bring up ALL traces at once (in a scrolling window) at a particular location. You can also have this feature on when navigating to consensus locations. Since POLYPHRED tags the consensus with polymorphism tags, you can navigate to those locations and conveniently determine if each site is a real polymorphism. Reads can be put into alphabetical order This is in addition to the sorting based on top strand/bottom strand and left clone end position. Show Protein Translation You can see this (if you like) in the Aligned Reads Window in all 6 reading frames Find Open Reading Frames --------------------------------------------------------------------- Add read name to a file with options Saves your last used options Windows raise when you want to see them When you navigate to a location, the window raises. When you use Compare Contigs and click on the second contig, the Compare Contigs Window raises to the top. Exporting part of the consensus and exporting quality Consed can write a part of the consensus, rather than the whole consensus. It can write just the bases, or it can write both the bases and the quality values. Aesthetic improvements for very large assemblies (over 10,000 reads) --------------------------------------------------------------------- For programmers only: Whole read items are now implemented Users can see these tags by clicking in the Aligned Reads Window on the read name with the right mouse button. Comment read tags are allowed in the ace file (RT tags) Consed parameters Now it is much easier to set/change consed resources. If you make a typo, consed will tell you. You can set project-specific resources by putting a file .consedrc into the same directory with the ace file. You can also set system-wide consed resources with the environment variable CONSED_PARAMETERS You can set user-specific resources in the file ~/.consedrc You no longer have to do xrdb -remove. Consed is now tolerant of missing or corrupted phd files Consed handles the missing phd file by reporting the error, making the read all quality 0 (dark), and not allowing you to pop up the trace or edit the read. Consed DEC alpha users: Type: uname -sr and see what it says. If anyone is still on the old OSF1 V3.2, let me know since I am considering dropping support for it. If it says OSF1 V4.0, don't worry--I'll continue to support that. You have to rev up to at least V4.0 for Y2K compliance. Consed Sun users: Type: uname -sr and see what it says. If anyone is still on the old 'SunOS 5.4', consed will still probably work, but I'm not guaranteeing anything. It it says 'SunOS 5.5.1' or 'SunOS 5.6' or 'SunOS 5.7', etc. don't worry--I'll continue to support those.