Consed 28.0 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. Included below: WHAT IS NEW WITH CONSED 28.0 HOW TO GET CONSED UPGRADING FROM CONSED 27.0 to 28.0 WHAT IS NEW WITH CONSED 28.0: This is the last version of consed that will support Redhat 4 Major new features: * Bionano digest support. This allows the user to see how the Bionano digest confirms or is discrepant with the assembly. For more detail, see the movie: http://bozeman.mbt.washington.edu/consed/bionano_demo/bionano_bamscape.mov * multiple BAM files in bamscape: each has a separate graph of read depth in a separate color. For instance, you can have PacBio read depth in one color and Illumina in another. * consed can read and write compressed ace files and phdballs * Aligned Reads Window now shows, for each read either I or C (part of an inconsistent or consistent mate pair), or U unpaired. If you point at the I, C, or U with the mouse, the status line will indicate how far apart the pair is, what the library name is, and what the mean and max insert size is for that library. * Jump to mate (available on right mouse popup menu) Minor new features: bam2Ace * can handle cigars from hell such as: 31S3I1M3D8M1D19M2I2M1D3M3D2M3I1M1D1M1D697M1D80M1D12M1D17M1I27M6S bamScape * speed up * "region cursor" that highlights a region showing where a problem region is * ability to hide/unhide clustered mates on same scaffold in the Swiped Region Window * When BamScape brings up consed on a targeted region, include *all* reads--do not use shallowerDepth (by default). * Inconsistent read depth: now shows just clustered so doesn't show most spurious (chimeric) inconsistent mate pairs. Now 2 separate graphs: one for mates in the same contig; one for mates in a different contig * Allows users to navigate by a custom navigation file, just as in consed consed (graphical editor) * Assembly View allows reads to be removed as a group, preserving the alignment between them * Assembly View: automatic restart after tears, joins, and miniassemblies * Next-Gen read editing: if phd_dir doesn't exist, create it to save edited read (instead of giving an error) * When going to a specific read, include horizontal line to the read name--handy when the window is large and there are many reads. * For making slides/snapshots of consed: make the trace window scale visible * Info/Depth of Coverage on Main Consed Window gives average depth of coverage for the entire assembly * Ability to edit an 454 read with a missing sff file * Fixing reads at top of Aligned Reads Window: not just one at a time, but all highlighted reads at once * Chromosome positions can be used not only for the consensus scale, but also for all Navigate lists and Search for String results. * Tearing contigs: an improved method of determining which reads will go into the new left contig and which into the new right * Room for read names in Aligned Reads Window doesn't vary with scrolling * "Find read by name" will no longer cause consed to scroll unnecessarily Batch features * Batch tear allowing you to specify multiple locations at once * consed -selectContigs to make a little ace file/phdball of just the reads in a few selected contigs * Reports: ability to specify the filename 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 8) If you downloaded the file on a Windows computer, transfer it to a linux or macosx computer before proceeding. 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. UPGRADING FROM CONSED 27.0 to 28.0 Since there is an installation script (see INSTALLING CONSED below), it is easiest to delete (or hide) your current distribution and follow the consed installation instructions (below). If you have customized some of consed's perl scripts, you might want to save some of them. Be aware, however, that the following perl scripts have changed: addReads2Consed.perl bam2Ace.perl convertBedToBamScape.perl fasta2Ace.perl picard2Regions.perl In addition, the executables and some of the sample datasets have changed. You will get the new ones by using the installation script.