We are redesigning parts of the website. Please do not get surprised, if the theme looks different.
We are at the end of January and were not able to keep up with promised commentaries on SOAPdenovo2. Privately we are continuing to play with the code, but did not get time to describe the pieces together in coherent articles. Those commentaries will continue to appear in February.
Here is our bigger objective. We plan to split all major assemblers into code components and mix and match them to assemble the fish library in Assemblathon 2, which was the hardest to assemble. We like to understand the results of Assemblathon 2 at the algorithmic level, and explain to our readers.
Our next SOAPdenovo2-related commentary describing the data structures will come next. Also note that Rayan Chikhi has been working on the scaffolding part of the code and updated SOAPdenovo2 wiki page with top-level description of how scaffolding runs.