What is new with Consed 22.0: -BamView is a new program that can display an overview of reads in a bam file very quickly and using very little memory. It can also bring up consed to view and edit targeted regions. It has graphs of read depth (with 0-read-depth regions labelled), depth of reads with inconsistently mapped mates, and a graph of the rate of discrepancies (including indels). These graphs enable you to find problem areas. Try this and tell me what you would like added--I want to make this meet your needs. -Create an ace file from a bam file: consed -bam2Ace You can make an ace file out of just a targeted region of the reference sequence or out of the entire reference sequence. Cigars are shown in consed. By default, shallowerDepth (below) is included. -ShallowerDepth: Takes a high depth of coverage assembly and makes a shallower depth of coverage assembly that preserves all variants as well as (optionally) keeping mate pairs. -Show and Make Potential Joins. Finds all potential joins between contigs and makes them. A semiautomated mode allows the user to review each and decide whether to make them. An automated mode simply makes all joins. -Assembly View is no longer a bloody mess--most of the spurious red lines have been removed and (hopefully) all of the serious red lines are still present -Ability to fix a read (or reads) at the top of the Aligned Reads Window...handy for following a particular read -Remove Reads: consensus bases (in addition to qualities) are recalculated after removing the reads. If no reads remain at a location, the user has a choice of whether to have the contig break into 2 contigs, or just have a location where there are no reads. You can also remove reads by specifying a sequence at a position--this can save a lot of work, for example, if there are hundreds of reads at a position and many of the reads don't belong there. -Fixing the consensus in batch: consed -fixConsensus Allows the user to conveniently review all of the changes. This can give the wrong answer if the reads are misaligned. -Depth of coverage at cursor can be printed -fasta2Ace.perl allows adding a polymorphism tag to each reference sequence indicating the site of a snp -Miniassemblies will screen 454 reads for vector -Search for Highly Discrepant Positions used to stop 10 times if a read had a 10-base deletion like this ********** but now only stops once -Illumina mate pairs are now allowed to link contigs -Contigs that had high depth of coverage used to be excluded from scaffolds. No longer (by default). -Tags are not duplicated when tearing a contig or doing miniassemblies -Complementing contigs in batch (consed -complementContigs) -Exporting scaffolds in batch. Contigs that are ordered and oriented are output with a fixed # of N's between them. Options for fastq or fasta format and whether or not to trim the low quality ends of contigs. -Speed up for consed startup in which there are large #s of consensus tags. - consedrc can now be used instead of .consedrc Retiring: Consed no longer shows the Golden Path (in colormode "color means match") This will be the last release in which we will support Itanium computers, and we will not support any bugs that are specific to Itanium computers.