Consed is the finishing portion of the Phred/Phrap/Consed package. Consed 19.0 is now available. Every Consed site should immediately discontinue using older versions of Consed. Older versions of Consed have bugs fixed in Consed 19.0 and are no longer supported. Consed 19.0 is an emergency maintenance release: -It fixes a problem with "Add New Reads" that causes consed to refuse to continue to add new reads. Instead, it gives an error message like this: Inserting pads in contigs to accommodate insertions in new reads...base segment from padded cons pos 1061 to 1127 is not within read E765WZ105C3VBK which lies within padded cons pos 1062 to 1350 exception thrown: addNewReads.cpp:1573 Failed assertion 'pContig->baseSegArray_.bGetDataStructureOk()' Thanks to Cliff Han (LANL) and Andre Villegas (Public Health of Canada) for supplying me with datasets to fix this. -It fixes a minor problem with tagRepeats.perl -It supports paired Solexa reads in Assembly View. Read the documentation for adding Solexa reads. The only difference is that in the file for listing the fastq files of Solexa reads to be added, instead of: > more solexa_files.fof solexa_lane1.fastq solexa_lane2.fastq solexa_lane3.fastq . . . the fof file contains: solexa_lane1_1.fastq solexa_lane1_2.fastq solexa_lane2_1.fastq solexa_lane2_2.fastq solexa_lane3_1.fastq solexa_lane3_2.fastq . . . where solexa_lane1_1.fastq and solexa_lane1_2.fastq contain the /1 and /2 reads respectively. Thanks to Joe Fass, UC Davis, for sample datasets for this. For more information on any of these features, see http://bozeman.mbt.washington.edu/consed/distributions/README.19.0.txt or the README.txt which is part of the .tar.gz file you download (see below). HOW TO GET CONSED: 1) If we have already given you web access, you will still have that access and can proceed to step 6) 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 dgordon (-AT-) u.washington.edu with the following 3 pieces of information: A) which type of operating system you are running: linux (32 bit), linux (64 bit) (intel, amd, or EM64T), linux (itanium), macosx, solaris (on sparc), solaris-intel. (Consed is not available for Windows.) B) which version of the operating system (above) C) what the following web site says: http://bozeman.mbt.washington.edu/consed/find_ip_address.html This 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 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. If you think your external ip address starts with "10.", you are wrong.) 5) Wait for me to send you back a message that you have access. Wait for this response before proceeding to step 5. It can take up to 2 weeks for processing, so please be patient. 6) Using firefox, Safari, Internet Explorer, 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., firefox) 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 browsers 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 dgordon (-AT- ) u.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 your browser, when you saved the file, what name you gave the file). zcat consed_linux.tar.gz | tar -xvf - zcat consed_solaris.tar.gz | tar -xvf - zcat consed_mac.tar.gz | tar -xvf - zcat consed_solaris_intel.tar.gz | 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 including the section labelled "INSTALLING CONSED". Also, you should read any notes from the following web site, if it exists: http://bozeman.mbt.washington.edu/consed/distributions/19.0_additional_info.txt (This is information added after the release was built.) All bug reports and suggestions for improvement are appreciated. 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. To use this version of consed, you will need a version of the phrap package (which includes cross_match) of 1.080721 or later (where "080721" means year 2008, month 07 (July) and the 21th day of the month and the leading "1." is ignored.) To request the most recent version of the phrap package, send an email to phg@u.washington.edu, with a Subject line that says "phrap new version request", and an email body that consists of the following two lines (it should be in exactly this format, to be computer readable): Request: phrap ver 1.080721 or later Registered phrap email address: [[insert address here]] The address should be the one you supplied previously when obtaining phrap; the new version will be sent to it. If you have not previously registered for phrap, or your registered address is no longer valid, you will need to include a license agreement (with all questions answered) in the email.