Pick your data:
- simulated single-end 100 bp reads
- simulated paired-end reads 2x100, one insert size (400 bp)
- simulated paired-end reads 2x100, two insert sizes (400 + 3000 bp)
- real data 2x100?
Run velvet:
velveth 63
Look at stats...
N50, assy size, max contig, % coding genes (wait for annotation), look at velvetContigStats in BioITeam/sphsmith
Extended: mira...
De Novo Assembly
De Novo asssembly is creating a genome without a reference genome. Creating a genome with a reference genome is called mapping assembly.
A list of assemblers can be found here.
We'll take a look at Velvet.
Velvet is available on Lonestar. Type:
module load velvet
