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. De-novo assemblies.
Standardized velvet assembly report from Jeremy Leipzig.
MetaVelvet for metagenomic assemblies.
MIRA for scaffolded assemblies.
Annotation resources:
RAST & MG-RAST for genomes and metagenomes respectively.
Microbial ecology:
QIIME from Rob Knight’s lab
Mothur from Pat Schloss’s lab.
