Our slug DNA is disappearing very quickly. Burn after reading? Convert illumina into something newbler can read.

trim9.goodlength.hist 

C is preferable to C++ even although both C and C++ would could be used as long as you are careful.

aligner.py = python module for global and local alignment, used in "find-dna-differences" 

find-dna-differences good for finding snips and indels between two assemblies. Outputs bed along with some other formats.
Can express snips and indels in "differences" format:
sequence:location:sequence


differences2stitcher 
kstitcher- stitches contigs together 

stitcher format:
@name comment
+contigname -contigname ... -(+contig17 -contig18) ... 15*N ... 12*(-contig8)... 

expr1 < expr2 > expr3 means "in expr1 replace the unique expr2 with expr3"