Recipes for Assembling Genomes from GAGE

Do you want to learn nice shortcuts for running various popular assembly programs? GAGE (Genome Assembly Gold-standard Evaluation) website is a good place to check (links below). For good set of tutorials on running Velvet, ABySS, Bowtie, BWA and Newbler, please check here.

ABYSS recipes

ALLPATHS-LG recipes

Bambus2 recipes

Celera Assembler recipes

MSR-CA recipes

SGA recipes

SOAPdenovo recipes

Velvet recipes