bowtie-build -C -f bowtie_index/cs/eschColi_CFT073.fa bowtie_index/eschColi_CFT073
bowtie-build -f bowtie_index/eschColi_CFT073.fa bowtie_index/eschColi_CFT073
bwa index -a bwtsw eschColi_CFT073.fa
samtools faidx eschColi_CFT073.fa
java -cp "/afs/bx.psu.edu/user/kpvincent/galaxy-data-tables/tool-data/shared/jars/srma.jar" net.sf.picard.sam.CreateSequenceDictionary R=eschColi_CFT073.fa O=eschColi_CFT073.dict URI=eschColi_CFT073.fa

