Consed 27.0 is now available for download. Consed is a visualization/finishing tool for read alignments and assemblies. Every Consed site should immediately discontinue using older versions of Consed and switch to this version. Older versions are no longer supported. What is new with Consed 27.0: * Two serious bugs (causing crashes) have been fixed. * new BAM file features - consed -findBamProblems reports clustered inconsistent mate pairs (also reports too high or too low depth of coverage, too high discrepancy rate, too high rate of inconsistent mate pairs). - this report is now sorted by severity so you can bring up bamScape and just look at, for example, the 20 most severe problem locations - bam2Ace handles BAM files with duplicate reads - bam2Ace evaluates clipped ends of multiple reads to see if they indicate an insertion in the read e.g., AGATATGAC*****AAAGAATAACCATGACCTT (reference) tttttAAAGAATAACCATCCCC...(a read) ...AGATATGACttttt (another read) ^^^^^ inserted region * In Consed's Aligned Reads Window, click then shift-click selects a large number of reads for removing (just as in Windows applications). Reads can also be selected based on sequence when tearing a contig. 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), macosx, solaris10 (on sparc). (Consed is not available for Windows.) B) which version of the operating system (above) C) what the following web site says on the computer you will use to download consed: http://bozeman.mbt.washington.edu/consed/find_unique_id.html (What is this number and why must you send it to me? This is a unique identifier you transmit to *any* web site you visit--you are not giving me any private information. This allows my web server to know that the request to download consed is coming from someone who has a license. Otherwise you will not be able to download consed. This number is often not the same as the real IP--you must use the http://bozeman.mbt.washington.edu/consed/find_unique_id.html to find this number. This number *never* starts with "10.") 5) Wait for me to send you back a message that you have access. Wait for this response before proceeding to step 6. It can take up to 2 weeks for processing, so please be patient. 6) Using firefox, Safari, Chrome, 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. 7) 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 If you downloaded the file on a Windows computer, transfer it to a linux or macosx computer before proceeding. 8) Unpack the consed bundle in its own subdirectory as follows: mkdir consed_download cd consed_download gunzip -c (whatever) | tar -xvf - The "whatever" depends on, in your browser when you saved the file, the name you gave the file. It also depends on where you are and where the file is. But will usually be one of the following: gunzip -c ../consed_linux.tar.gz | tar -xvf - gunzip -c ../consed_solaris.tar.gz | tar -xvf - gunzip -c ../consed_mac.tar.gz | tar -xvf - 9) You will now see a file README.txt in the current directory. Find the section labelled "INSTALLING CONSED" and follow its instructions. Also, you should read any notes from the following web site, if it exists: http://bozeman.mbt.washington.edu/consed/distributions/27.0_additional_info.txt (This is information added after the release was built.) 10) REQUIRED VERSION OF PHRAP TO WORK WITH CONSED You will need to specially request the most recent version of phrap--not the one that you get with a normal request. To request the most recent version of phrap and cross_match (cross_match comes with phrap), 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. This system is not completely automated so you may need to wait several days. 11) 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 less than 1 email messages per month on this list (with some months having 5 and most having none). All bug reports and suggestions for improvement are appreciated.