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