Resources
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:
Nick Loman’s xbase. For short read annotation and assembly. This goes hand in hand with his sage advice page. Also, this document from Illumina
Velvet, of course.
Standardized velvet assembly report from Jeremy Leipzig.
Annotation resources:
RAST & MG-RAST for genomes and metagenomes respectively.
Microbial ecology:
QIIME from Rob Knight’s lab
Mothur from Pat Schloss’s lab.
