Script mapping

#alignment
novoalign -F ILMFQ -t120 -r0.2 -q5 -d hg19Splices34.index -f 1.txt 2.txt > 84060.novoalign

#transform to MAQ
maq novo2maq 84060.novoalign.map - 84060.novoalign

#Convert the reference sequences to the binary fasta format
maq fasta2bfa ref.fasta ref.bfa

#Build the mapping assembly
maq assemble consensus.cns ref.bfa 84060.novoalign.map 2>assemble.log

#Extract consensus sequences and qualities
maq cns2fq consensus.cns >cns.fq

#Extract list of SNPs
maq cns2snp consensus.cns >cns.snp


will be translated to :


/PATH_TO_NONOALIGN/novoalign -F ILMFQ -t120 -r0.2 -q5 -d /PATH_TO_GENOME_INDEX/hg19Splices34.index -f /PATH_TO_INPUT_FILE/1.txt /PATH_TO_INPUT_FILE/2.txt > /PATH_TO_OUTPUT_FILE/1_84060.novoalign
/PATH_TO_MAQ/maq novo2maq /PATH_TO_OUTPUT_FILE/84060.novoalign.map - /PATH_TO_INPUT_FILE/84060.novoalign
...