Here is a list of the tools we are considering using for assembling and annotating the Banana Slug genome. Each of these listed tools will have their own page describing what the tool is supposed to do, and what we were able to get it to do.
Tools used on reads before assembly to improve assembly quality
The initial list of assembly tools was created from the Sequence Assembly page. However the links to the programs have been double checked, and some of them are different from those listed on the wikipedia page. — John St. John 2010/03/29 20:02
The only de-novo assemblers that can use Solid colorspace are Velvet (DBG) and Shorty (Overlap Concensus). CLC bio’s de novo assembler uses Solid reads in a limited way for mate-paired resolution of contigs only.
Here is an analysis of assemblers that used many of the assembler we are looking into. It includes “recipes” for how they ran each assembler.
Tools used to map reads or contigs onto contigs, scaffolds, or genomes.