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.