WHAT IS NEW IN CONSED 18.0


Speedup
    Speeding up removing reads
    Faster start up for many solexa reads
    
Paired-end 454 Reads
    You supply an sff file and consed will appropriately form the paired
    reads, just as Newbler does.

Assembly View
    Much faster
    More options

Consed for MAC
    Consed is now much faster on Intel-based macs since
    there is now a native executable

Recalculate consensus quality values when adding new reads
    Supports Solexa and 454 reads and is about 50x faster

Removing all reads in a contig(s)
    You can do this from either the graphical interface or from
    a script.
    
Fixed many bugs in consed 17 including those involved with:
    -nophd 
    Joining contigs
    Adding Sanger reads and bringing up traces

Cross_match (available separately from Consed-see below)
    This familiar gapped alignment tool is now so fast that it can be
    used as a genome search engine.  For example, a million solexa
    reads can be searched against the entire (repeat masked) human
    genome in less than an hour for most desktop computers and
    datasets.  Consed-ready ace files can be prepared in a fraction
    more time.  Peak memory usage: 4 to 5 Gb.

    Reports sequence variants & confirmed segments and strength of
    evidence, for resequencing applications

    Local, Global, Semi-global, and spliced (RNAseq) alignments

    Flexible reporting of hits: all, single top, all top, 
    or top if sufficiently better than others