Build Genome Index

#novoalign

#normal

novoindex -k 14 -s 1 hg19.nov.normal.nix hg19.fasta

#solid color space

novoindex -k 14 -s 1 -c hg19.nov.color.nix hg19.fasta

#bisulphite

novoindex -k 14 -s 1 -b hg19.nov.bis.nix hg19.fasta

#normal

bwa index -a bwtsw -p hg19.bwa.normal hg19.fasta

#color

bwa index -a bwtsw -c -p hg19.bwa.color hg19.fasta

wget http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/chr*.fa.gz

novoindex -k 14 -s 1 mm9.nov.normal.nix genomes/mm9/fasta/mm9.fasta

novoindex -k 14 -s 1 -c mm9.nov.color.nix genomes/mm9/fasta/mm9.fasta

novoindex -k 14 -s 1 -b mm9.nov.bis.nix genomes/mm9/fasta/mm9.fasta

#normal

./bwa index -a bwtsw -p mm9.bwa.normal genomes/mm9/fasta/mm9.fasta

./bwa index -a bwtsw -c -p mm9.bwa.color genomes/mm9/fasta/mm9.fasta