Simulate data for pipeline

Organsim, CE6

#download

wget http://sourceforge.net/projects/maq/files/maq-data/20080929/calib-36.dat.gz/download

#unzip

gzip -d calib-36.dat.gz

#simulate reads

maq simulate ce6_1.fq ce6_2.fq ce6.fa calib-36.dat

#make indexed genome

novoindex ce6.ndx ce6.fa

#Align reads to ce6 genome

time novoalign -d ce6.ndx -d ce6_1.fq ce6_2.fq | grep chr > A.ce6.nal

real 1m43.108s

user 6m39.372s

sys 0m4.652s

#Format to MAQ

novo2maq A.map - A.ce6.nal

#Convert the reference sequences to the binary fasta format

#maq fasta2bfa ref.fasta ref.bfa

#Build the mapping assembly

maq assemble A.cns ref.bfa A.map 2>assemble.log

#Extract consensus sequences and qualities

maq cns2fq A.cns >A.cns.fq

#Extract list of SNPs

maq cns2snp A.cns >A.snp