I need one page to collate software and docs I come across, and that is or might be useful to me. Let’s hope this does not become a total mess, and would be useful to others.
Short read assembly:
Velvet, of course. De-novo assemblies.
MetaVelvet for metagenomic assemblies.
MIRA for scaffolded assemblies.
QIIME from Rob Knight’s lab
Mothur from Pat Schloss’s lab.