Consed is the finishing portion of the Phred/Phrap/Consed package. HOW TO GET CONSED: 1) If we have already given you web access, you will still have that access and can proceed to step 5) to download the new version. If we have not yet given you web access: 2) If you are an academic user, get a copy of the academic agreement from: http://bozeman.mbt.washington.edu/consed/academic_agreement.txt and follow the instructions. This agreement basically says that you will not use Phred/Phrap/Consed for any commercial purpose, including commercially funded sequencing and that you agree not to allow anyone who does not have a license to access the software. 3) If you are a commercial user, there is a fee (to help support further Phred/Phrap/Consed development) and you should email swxfr@u.washington.edu You can get Phred/Phrap/Consed quite rapidly if you sign the commercial license agreement without making any modifications. 4) Whether you are an academic user or commercial user, you must send an email message to gordon (-AT-) genome.washington.edu with the following 2 pieces of information: A) which type and version of operating system you are running (solaris 2.5.1, 2.6, 7, 8, 9, alpha 3.7, 4.0, ibm aix 5.1 or better, solaris-intel 8 or better, macosx Darwin Kernel 6.5 or better, or linux intel with kernel 2.4, 2.5, or 2.6 (and which flavor of linux), linux Itanium 64 bit, AMD64 B) Please view page http://bozeman.mbt.washington.edu/consed/find_ip_address.html which will tell you what ip address you are transmitting. This ip address is the ip address that you transmit to any web site you access and it is my method of allowing access to you without allowing access to everyone. You should view the page above from the the computer on which you will be running a web browser to download consed. This does not have to be the same computer as the one on which you will run consed. (Even if you think you know your ip address, firewalls and proxies can cause your browser to transmit a different ip address, and thus my webserver would deny you access to consed. So it would be a good idea to view the page above and send me the ip address it shows, even if this isn't your real ip address.) I will send you back a message that you have access. Wait for this response before proceding to step 5. 5) Using netscape, firefox, or some other browser on the computer of which you used for step 4, open url: http://bozeman.mbt.washington.edu/consed/consed.html#howToGet Click on the appropriate type of computer. Your browser (e.g., netscape) will ask you what you want to name the file. Just use the default. If you are denied access, *carefully* follow the instructions on the "Don't have a cow, man--You are not authorized to get this document" page, including the try-to-get-consed part. Please do not email David Gordon until after you have followed these instructions. 6) Some people have had problems with netscape timing out and closing the file before they have completely received it. This problem is unlikely to occur now. But to be sure, type: ls -l to see the size of the transferred file. Look on the web page to see how large the transferred file should be. If the file is not completely transferred, then try again. If you try 3 times and still can't get a complete copy, notify me at gordon (-AT- ) genome.washington.edu 7) Transfer the file to a UNIX (not a Windows) computer. Then type whichever of the following is appropriate for you. (This depends on, in netscape, when you saved the file, what name you gave the file). zcat consed_linux.tar.Z | tar -xvf - zcat consed_linux_itanium.tar.Z | tar -xvf - zcat consed_solaris.tar.Z | tar -xvf - zcat consed_mac.tar.Z | tar -xvf - zcat consed_ibm.tar.Z | tar -xvf - zcat consed_alpha.tar.Z | tar -xvf - zcat consed_solaris_intel.tar.Z | tar -xvf - zcat consed_amd64.tar.Z | tar -xvf - Note: You must run tar on a UNIX computer--not on an Windows computer, due to a difference in the handling of breaks between lines. 8) Follow the instructions in README.txt included the section labelled "INSTALLING CONSED". Also, you should read any notes from the following web site: http://bozeman.mbt.washington.edu/consed/distributions/16.0_additional_info.txt (This is information added after the release was built.) All bug reports and suggestions for improvement are appreciated. You MUST have the following versions in order to use this version of Consed: (to find the version, you can usually type "(program name) -V") 0.000925.c or later for phred 0.990319 or later for phrap and crossmatch 0.990622.e or later for phd2fasta (supplied with this version of consed) any version of addReads2Consed.perl (supplied with this version of consed) 030415 of phredPhrap (supplied with this version of consed) (Note: if you have an older version of phredPhrap, some of the more recent Consed features, such as miniassemblies, will not work. Note to existing polyphred users: phredPhrap now calls polyphred with different parameters which will give cause it to apply different tags than it used to, but these different tags will give it behavior consistent with that described below in CONSED-POLYPHRED INTERACTION. For more information, see http://droog.gs.washington.edu/PolyPhred.html ) 030117 or later for transferConsensusTags.perl (supplied with this version of consed) any version of tagRepeats.perl (supplied with this version of consed) any version of determineReadTypes.perl (or your own custom modified version) If you are using polyphred, you must have polyphred 3.5 or more recent. USING AN OLDER VERSION OF POLYPHRED WILL CAUSE SEVERE PROBLEMS WITH CONSED WHICH WILL APPEAR AS PROBLEMS WITH FILETYPES. Everything that comes with this version of Consed should replace any of your files that have the same name (unless you really know what you are doing). For Phred, contact bge@u.washington.edu (Brent Ewing) For Phrap and Crossmatch, contact phg@u.washington.edu (Phil Green) In order to run the gauntlet of Phred/phd2fasta/Crossmatch/Phrap, there is a perl script phredPhrap supplied with Consed (above). YOU MUST USE THIS PERL SCRIPT. If you try to run each of these programs directly, you are on your own and you will probably fail. 9) You may join PHUI, the Phred-Phrap-Consed-Autofinish email users' group. This email list is for people to post questions/problems with Phred-Phrap-Consed-Autofinish for other users to answer. To subscribe to PHUI, see: http://mailman.u.washington.edu/mailman/listinfo/phui At this time, there is an average of 2 email messages per month on this list. Consed 16.0 is now available. Every Consed site should immediately discontinue using older versions of Consed that have bugs fixed in Consed 16.0. Older versions of Consed are no longer supported. If you have modified some of the perl scripts--no problem. In that case, just upgrade the consed executable. WHAT IS NEW IN CONSED 16.0 454 reads can now be converted to scf files for viewing and editing in Consed Editing All reads can be changed at once to agree with a particular read (useful for quickly editing 454 reads to agree with an ABI read) Assembly View sometimes you are interested only in sequence matches (the black and orange lines) which indicate a potential join. The other lines (internal matches) clutter up the picture. Now you can show (optionally) just the lines that connect ends of contigs. Compare Contigs Window you used to have to scroll back and forth looking for discrepancies. Now you can now click "next" and "previous" to go to each successive discrepancy between contigs. You can also see the # of discrepancies and the discrepancy rate. Add New Reads there is now a navigation file so you can visit the location of each added read. Tags * In the past you could navigate by a tag type (e.g., all dataNeeded tags). Now you can navigate by several tag types, and there is a convenient method of selecting a large group of tag types. * You can search for an oligo tag by the name of the oligo. * Once you found an oligo tag, you can search the assembly for any location that matches the bases in that oligo (to find other locations matching that sequence--this could happen if the assembly has changed) * Can easily add a tag to each read at a position (useful for polymorphism work) AutoReport can print out all contig-linking forward/reverse read pairs See README.txt for more information on any of these new features.