What is new with Consed 24.0: -bamScape allows searching for problem locations in a BAM file, such as: too high (or too low) depth of coverage too high % and # of reads with inconsistently placed mates too high % and # of reads that are discrepant with the reference Problems can be saved in an interactive list (clicking on a list item scrolls the display to that location) or in a file. BamScape can start up with this list pre-loaded. -bamScape can start consed allowing the user to edit targeted locations of the reference. rewriteReference can be run to generate a new (corrected) copy of the reference sequence. -bam2Ace is improved in various ways such as including reads that protrude from the specified region -consed can display tracks (similar to IGV or UCSC Genome Browser) including gene tracks (showing untranslated regions, introns, and translated regions with amino acid translation) and conservation tracks (bars of different shades of grey) and custom tracks See this demonstration (movie) of this feature: http://www.phrap.org/consed/tracks_demo/bed_tracks_in_consed3.mov -consed can detect SNP's using Li and Durbin's probabilistic method 3 interfaces: navigate by snps in entire assembly find genotype at cursor location autoreport generates a VCF file in batch includes indels -Add New Reads feature allows the user to specify an approximate location for the read to be added -RNA-Seq alignments. Allows jumping between splice sites. -When removing reads, mates of these reads can optionally also be removed -ability to edit any read (Illumina, 454, Sanger) -highlight features: highlight all reads at cursor with particular base sequence; unhighlight all reads; remove highlighted reads; save highlighted read names to file; highlight mates of highlighted reads; tear contig uses highlighted reads; etc.